diff --git a/src/gmt_init.c b/src/gmt_init.c
index 182e31c94ae..de0f2b5783f 100644
--- a/src/gmt_init.c
+++ b/src/gmt_init.c
@@ -4072,7 +4072,7 @@ GMT_LOCAL int gmtinit_split_info_strings (struct GMT_CTRL *GMT, const char *in,
 }
 
 /*! . */
-GMT_LOCAL int gmtinit_init_custom_annot (struct GMT_CTRL *GMT, struct GMT_PLOT_AXIS *A, int *n_int) {
+GMT_LOCAL int gmtinit_init_custom_annot (struct GMT_CTRL *GMT, struct GMT_PLOT_AXIS *A, int *n_int, char *filename) {
 	/* Reads a file with one or more records of the form
 	 * value	types	[label]
 	 * where value is the coordinate of the tickmark, types is a combination
@@ -4080,6 +4080,7 @@ GMT_LOCAL int gmtinit_init_custom_annot (struct GMT_CTRL *GMT, struct GMT_PLOT_A
 	 * The a|i will take a label string (or sentence).
 	 * The item argument specifies which type to consider [a|i,f,g].  We return
 	 * an array with coordinates and labels, and set interval to true if applicable.
+	 * filename is the custom annotation file to read (either primary or secondary).
 	 */
 	int error, k, n_errors = 0;
 	bool save_trailing;
@@ -4099,7 +4100,7 @@ GMT_LOCAL int gmtinit_init_custom_annot (struct GMT_CTRL *GMT, struct GMT_PLOT_A
 	GMT->current.io.trailing_text[GMT_IN] = true;
 	GMT->current.io.max_cols_to_read = 1;
 	if ((error = GMT_Set_Columns (GMT->parent, GMT_IN, 1, GMT_COL_FIX)) != GMT_NOERROR) return (1);
-	if ((D = GMT_Read_Data (GMT->parent, GMT_IS_DATASET, GMT_IS_FILE, GMT_IS_NONE, GMT_READ_NORMAL, NULL, A->file_custom, NULL)) == NULL) {
+	if ((D = GMT_Read_Data (GMT->parent, GMT_IS_DATASET, GMT_IS_FILE, GMT_IS_NONE, GMT_READ_NORMAL, NULL, filename, NULL)) == NULL) {
 		gmt_set_column_type (GMT, GMT_IN, GMT_X, save_coltype);
 		return (1);
 	}
@@ -4119,7 +4120,7 @@ GMT_LOCAL int gmtinit_init_custom_annot (struct GMT_CTRL *GMT, struct GMT_PLOT_A
 	for (row = 0; row < S->n_rows; row++) {
 		k = sscanf (S->text[row], "%s", type);
 		if (k != 1) {
-			GMT_Report (GMT->parent, GMT_MSG_ERROR, "Bad format record [%s] at row %d in custom file %s.\n", S->text[row], (int)row, A->file_custom);
+			GMT_Report (GMT->parent, GMT_MSG_ERROR, "Bad format record [%s] at row %d in custom file %s.\n", S->text[row], (int)row, filename);
 			n_errors++;
 			continue;
 		}
@@ -4138,7 +4139,7 @@ GMT_LOCAL int gmtinit_init_custom_annot (struct GMT_CTRL *GMT, struct GMT_PLOT_A
 					n_int[GMT_ITEM_GRID]++;
 					break;
 				default:
-					GMT_Report (GMT->parent, GMT_MSG_ERROR, "Unrecognized type (%c) at row %d in custom file %s.\n", type[k], (int)row, A->file_custom);
+					GMT_Report (GMT->parent, GMT_MSG_ERROR, "Unrecognized type (%c) at row %d in custom file %s.\n", type[k], (int)row, filename);
 					n_errors++;
 					break;
 			}
@@ -4146,9 +4147,9 @@ GMT_LOCAL int gmtinit_init_custom_annot (struct GMT_CTRL *GMT, struct GMT_PLOT_A
 	}
 	GMT_Destroy_Data (GMT->parent, &D);
 
-	GMT_Report (GMT->parent, GMT_MSG_DEBUG, "Processed custom annotations via %s for axis %d.\n", A->file_custom, A->id);
+	GMT_Report (GMT->parent, GMT_MSG_DEBUG, "Processed custom annotations via %s for axis %d.\n", filename, A->id);
 	if (n_int[GMT_ITEM_ANNOT] && n_int[GMT_ITEM_INTVAL]) {
-		GMT_Report (GMT->parent, GMT_MSG_ERROR, "Cannot mix interval and regular annotations in custom file %s.\n", A->file_custom);
+		GMT_Report (GMT->parent, GMT_MSG_ERROR, "Cannot mix interval and regular annotations in custom file %s.\n", filename);
 		n_errors++;
 	}
 	return (n_errors);
@@ -4315,12 +4316,13 @@ GMT_LOCAL int gmtinit_decode_tinfo (struct GMT_CTRL *GMT, int axis, char flag, c
 
 	if (flag == 'c') {	/* Custom annotation arrangement */
 		int k, n_int[GMT_N_AXIS_ITEMS];
+		unsigned int pi = GMT->current.map.frame.primary ? 0 : 1;	/* 0 = primary, 1 = secondary */
 		char *list = "aifg";
 		if (!(gmt_access (GMT, &in[1], R_OK))) {
-			gmt_M_str_free (A->file_custom);
-			A->file_custom = strdup (&in[1]);
+			gmt_M_str_free (A->file_custom[pi]);
+			A->file_custom[pi] = strdup (&in[1]);
 			A->special = GMT_CUSTOM;
-			if (gmtinit_init_custom_annot (GMT, A, n_int)) return (GMT_NOTSET);	/* See what ticks, anots, gridlines etc are requested */
+			if (gmtinit_init_custom_annot (GMT, A, n_int, A->file_custom[pi])) return (GMT_NOTSET);	/* See what ticks, anots, gridlines etc are requested */
 			for (k = 0; k < GMT_N_AXIS_ITEMS; k++) {
 				if (n_int[k] == 0) continue;
 				flag = list[k];
@@ -4328,10 +4330,10 @@ GMT_LOCAL int gmtinit_decode_tinfo (struct GMT_CTRL *GMT, int axis, char flag, c
 				if ((error = gmtinit_set_titem (GMT, A, "0", flag, str[axis], true)))	/* Store the findings for this segment */
 					return (error);
 			}
-			if (n_int[GMT_ITEM_ANNOT])  A->item[GMT_ANNOT_UPPER].special = true;	/* custom annotations selected */
-			if (n_int[GMT_ITEM_INTVAL]) A->item[GMT_ANNOT_UPPER+!GMT->current.map.frame.primary].special = true;	/* custom interval annotations selected */
-			if (n_int[GMT_ITEM_TICK])   A->item[GMT_TICK_UPPER+!GMT->current.map.frame.primary].special = true;	/* custom tick annotations selected */
-			if (n_int[GMT_ITEM_GRID])   A->item[GMT_GRID_UPPER+!GMT->current.map.frame.primary].special = true;	/* custom gridlines selected */
+			if (n_int[GMT_ITEM_ANNOT])  A->item[GMT_ANNOT_UPPER+pi].special = true;	/* custom annotations selected */
+			if (n_int[GMT_ITEM_INTVAL]) A->item[GMT_ANNOT_UPPER+pi].special = true;	/* custom interval annotations selected */
+			if (n_int[GMT_ITEM_TICK])   A->item[GMT_TICK_UPPER+pi].special = true;	/* custom tick annotations selected */
+			if (n_int[GMT_ITEM_GRID])   A->item[GMT_GRID_UPPER+pi].special = true;	/* custom gridlines selected */
 			if (axis == GMT_Z)
 				GMT->current.map.frame.drawz = true;
 			else
diff --git a/src/gmt_internals.h b/src/gmt_internals.h
index e03f4346949..111ede38867 100644
--- a/src/gmt_internals.h
+++ b/src/gmt_internals.h
@@ -85,7 +85,7 @@ EXTERN_MSC double gmtlib_distance_type (struct GMT_CTRL *GMT, double lonS, doubl
 EXTERN_MSC bool gmtlib_genper_reset (struct GMT_CTRL *GMT, bool reset);
 EXTERN_MSC double gmtlib_left_boundary (struct GMT_CTRL *GMT, double y);
 EXTERN_MSC double gmtlib_right_boundary (struct GMT_CTRL *GMT, double y);
-EXTERN_MSC unsigned int gmtlib_load_custom_annot (struct GMT_CTRL *GMT, struct GMT_PLOT_AXIS *A, char item, double **xx, char ***labels);
+EXTERN_MSC unsigned int gmtlib_load_custom_annot (struct GMT_CTRL *GMT, struct GMT_PLOT_AXIS *A, char item, double **xx, char ***labels, unsigned int which);
 EXTERN_MSC int gmtlib_report_error	(void *C, int error);	/* Lives in gmt_api.c */
 EXTERN_MSC void gmtlib_iobl (struct GMT_CTRL *GMT, double *lon, double *lat, double olon, double olat);	/* Convert oblique lon/lat to regular lon/lat */
 EXTERN_MSC char *gmtlib_create_header_item (struct GMTAPI_CTRL *API, unsigned int mode, void *arg);
diff --git a/src/gmt_plot.c b/src/gmt_plot.c
index 005efe16a42..e04fc012770 100644
--- a/src/gmt_plot.c
+++ b/src/gmt_plot.c
@@ -2021,7 +2021,7 @@ GMT_LOCAL void gmtplot_map_gridlines (struct GMT_CTRL *GMT, struct PSL_CTRL *PSL
 
 		gmt_setpen (GMT, &GMT->current.setting.map_grid_pen[k]);
 
-		if (A[GMT_X]->item[item[k]].special && (np = gmtlib_load_custom_annot (GMT, &GMT->current.map.frame.axis[GMT_X], 'g', &v, NULL))) {
+		if (A[GMT_X]->item[item[k]].special && (np = gmtlib_load_custom_annot(GMT, &GMT->current.map.frame.axis[GMT_X], 'g', &v, NULL, k))) {
 			gmtplot_x_grid (GMT, PSL, s, n, v, np);
 			gmt_M_free (GMT, v);
 		}
@@ -2037,7 +2037,7 @@ GMT_LOCAL void gmtplot_map_gridlines (struct GMT_CTRL *GMT, struct PSL_CTRL *PSL
 		else	/* Draw grid lines that go S to N */
 			gmt_linearx_grid (GMT, PSL, w, e, s, n, dx);
 
-		if (A[GMT_Y]->item[item[k]].special && (np = gmtlib_load_custom_annot (GMT, &GMT->current.map.frame.axis[GMT_Y], 'g', &v, NULL))) {
+		if (A[GMT_Y]->item[item[k]].special && (np = gmtlib_load_custom_annot(GMT, &GMT->current.map.frame.axis[GMT_Y], 'g', &v, NULL, k))) {
 			gmtplot_y_grid (GMT, PSL, w, e, v, np);
 			gmt_M_free (GMT, v);
 		}
@@ -2352,8 +2352,8 @@ GMT_LOCAL void gmtplot_map_tickitem (struct GMT_CTRL *GMT, struct PSL_CTRL *PSL,
 
 	if (! (GMT->current.map.frame.axis[GMT_X].item[item].active || GMT->current.map.frame.axis[GMT_Y].item[item].active)) return;
 
-	dx = (GMT->current.map.frame.axis[GMT_X].file_custom) ? 1.0 : gmtlib_get_map_interval (GMT, GMT->current.map.frame.axis[GMT_X].type, &GMT->current.map.frame.axis[GMT_X].item[item]);
-	dy = (GMT->current.map.frame.axis[GMT_Y].file_custom) ? 1.0 : gmtlib_get_map_interval (GMT, GMT->current.map.frame.axis[GMT_Y].type, &GMT->current.map.frame.axis[GMT_Y].item[item]);
+	dx = (GMT->current.map.frame.axis[GMT_X].file_custom[item & 1]) ? 1.0 : gmtlib_get_map_interval(GMT, GMT->current.map.frame.axis[GMT_X].type, &GMT->current.map.frame.axis[GMT_X].item[item]);
+	dy = (GMT->current.map.frame.axis[GMT_Y].file_custom[item & 1]) ? 1.0 : gmtlib_get_map_interval(GMT, GMT->current.map.frame.axis[GMT_Y].type, &GMT->current.map.frame.axis[GMT_Y].item[item]);
 
 	if (dx <= 0.0 && dy <= 0.0) return;
 
@@ -2369,7 +2369,7 @@ GMT_LOCAL void gmtplot_map_tickitem (struct GMT_CTRL *GMT, struct PSL_CTRL *PSL,
 	GMT->current.map.on_border_is_outside = true;	/* Temporarily, points on the border are outside */
 
 	if (do_x) {	/* Draw grid lines that go E to W */
-		if (GMT->current.map.frame.axis[GMT_X].file_custom)
+		if (GMT->current.map.frame.axis[GMT_X].file_custom[item & 1])
 			nx = gmtlib_coordinate_array (GMT, w, e, &GMT->current.map.frame.axis[GMT_X].item[item], &val, NULL);
 		else
 			nx = gmtlib_linear_array (GMT, w, e, dx, GMT->current.map.frame.axis[GMT_X].phase, &val);
@@ -2382,7 +2382,7 @@ GMT_LOCAL void gmtplot_map_tickitem (struct GMT_CTRL *GMT, struct PSL_CTRL *PSL,
 
 	if (do_y) {	/* Draw grid lines that go S to N */
 		if (GMT->current.proj.z_down) {
-			if (GMT->current.map.frame.axis[GMT_Y].file_custom)
+			if (GMT->current.map.frame.axis[GMT_Y].file_custom[item & 1])
 				ny = gmtlib_coordinate_array (GMT, 0.0, GMT->current.proj.z_radius-s, &GMT->current.map.frame.axis[GMT_Y].item[item], &val, NULL);
 			else if (GMT->current.proj.z_down == GMT_ZDOWN_Z) /* z = n - r */
 				ny = gmtlib_linear_array (GMT, 0.0, GMT->current.proj.z_radius-s, dy, GMT->current.map.frame.axis[GMT_Y].phase, &val);
@@ -2396,7 +2396,7 @@ GMT_LOCAL void gmtplot_map_tickitem (struct GMT_CTRL *GMT, struct PSL_CTRL *PSL,
 			}
 		}
 		else {
-			if (GMT->current.map.frame.axis[GMT_Y].file_custom)
+			if (GMT->current.map.frame.axis[GMT_Y].file_custom[item & 1])
 				ny = gmtlib_coordinate_array (GMT, s, n, &GMT->current.map.frame.axis[GMT_Y].item[item], &val, NULL);
 			else
 				ny = gmtlib_linear_array (GMT, s, n, dy, GMT->current.map.frame.axis[GMT_Y].phase, &val);
@@ -2520,7 +2520,7 @@ GMT_LOCAL void gmtplot_consider_internal_annotations (struct GMT_CTRL *GMT, stru
 		}
 
 		if (GMT->current.proj.z_down) {	/* Want to annotate depth rather than radius */
-			if (GMT->current.map.frame.axis[GMT_Y].file_custom)
+			if (GMT->current.map.frame.axis[GMT_Y].file_custom[0])
 				ny = gmtlib_coordinate_array (GMT, 0.0, GMT->current.proj.z_radius-s, &GMT->current.map.frame.axis[GMT_Y].item[GMT_ANNOT_UPPER], &tval, &label_c);
 			else if (GMT->current.proj.z_down == GMT_ZDOWN_Z) /* z = n - r */
 				ny = gmtlib_linear_array (GMT, 0.0, GMT->current.proj.z_radius-s, dy, GMT->current.map.frame.axis[GMT_Y].phase, &tval);
@@ -2535,7 +2535,7 @@ GMT_LOCAL void gmtplot_consider_internal_annotations (struct GMT_CTRL *GMT, stru
 			}
 		}
 		else {				/* Annotate radius */
-			if (GMT->current.map.frame.axis[GMT_Y].file_custom)
+			if (GMT->current.map.frame.axis[GMT_Y].file_custom[0])
 				ny = gmtlib_coordinate_array (GMT, s, n, &GMT->current.map.frame.axis[GMT_Y].item[GMT_ANNOT_UPPER], &val, &label_c);
 			else
 				ny = gmtlib_linear_array (GMT, s, n, dy, GMT->current.map.frame.axis[GMT_Y].phase, &val);
@@ -2615,7 +2615,7 @@ GMT_LOCAL void gmtplot_consider_internal_annotations (struct GMT_CTRL *GMT, stru
 		do_minutes = (fabs (fmod (dx, 1.0)) > GMT_CONV4_LIMIT);
 		do_seconds = gmtlib_set_do_seconds (GMT, dx);
 
-		if (GMT->current.map.frame.axis[GMT_X].file_custom)
+		if (GMT->current.map.frame.axis[GMT_X].file_custom[0])
 			nx = gmtlib_coordinate_array (GMT, w, e, &GMT->current.map.frame.axis[GMT_X].item[GMT_ANNOT_UPPER], &val, &label_c);
 		else
 			nx = gmtlib_linear_array (GMT, w, e, dx, GMT->current.map.frame.axis[GMT_X].phase, &val);
@@ -2815,8 +2815,10 @@ GMT_LOCAL void gmtplot_map_annotate (struct GMT_CTRL *GMT, struct PSL_CTRL *PSL,
 	else
 		dy[0] = dy[1] = 0.0;
 
-	if (GMT->current.map.frame.axis[GMT_X].file_custom) dx[0] = 1.0;	/* To pass checks below */
-	if (GMT->current.map.frame.axis[GMT_Y].file_custom) dy[0] = 1.0;	/* To pass checks below */
+	if (GMT->current.map.frame.axis[GMT_X].file_custom[0]) dx[0] = 1.0;	/* To pass checks below */
+	if (GMT->current.map.frame.axis[GMT_X].file_custom[1]) dx[1] = 1.0;	/* Secondary custom file also needs valid interval */
+	if (GMT->current.map.frame.axis[GMT_Y].file_custom[0]) dy[0] = 1.0;	/* To pass checks below */
+	if (GMT->current.map.frame.axis[GMT_Y].file_custom[1]) dy[1] = 1.0;	/* Secondary custom file also needs valid interval */
 
 	if (dx[0] <= 0.0 && dy[0] <= 0.0) return;
 
@@ -2848,8 +2850,8 @@ GMT_LOCAL void gmtplot_map_annotate (struct GMT_CTRL *GMT, struct PSL_CTRL *PSL,
 			do_minutes = (fabs (fmod (dx[k], 1.0)) > GMT_CONV4_LIMIT);
 			do_seconds = gmtlib_set_do_seconds (GMT, dx[k]);
 
-			if (GMT->current.map.frame.axis[GMT_X].file_custom)
-				nx = gmtlib_coordinate_array (GMT, w, e, &GMT->current.map.frame.axis[GMT_X].item[GMT_ANNOT_UPPER], &val, &label_c);
+			if (GMT->current.map.frame.axis[GMT_X].file_custom[k])
+				nx = gmtlib_coordinate_array(GMT, w, e, &GMT->current.map.frame.axis[GMT_X].item[GMT_ANNOT_UPPER+k], &val, &label_c);
 			else
 				nx = gmtlib_linear_array (GMT, w, e, dx[k], GMT->current.map.frame.axis[GMT_X].phase, &val);
 			last = nx - 1;
@@ -2911,8 +2913,8 @@ GMT_LOCAL void gmtplot_map_annotate (struct GMT_CTRL *GMT, struct PSL_CTRL *PSL,
 			}
 
 			if (GMT->current.proj.z_down) {	/* Want to annotate depth rather than radius */
-				if (GMT->current.map.frame.axis[GMT_Y].file_custom)
-					ny = gmtlib_coordinate_array (GMT, 0.0, GMT->current.proj.z_radius-s, &GMT->current.map.frame.axis[GMT_Y].item[GMT_ANNOT_UPPER], &tval, &label_c);
+				if (GMT->current.map.frame.axis[GMT_Y].file_custom[k])
+					ny = gmtlib_coordinate_array(GMT, 0.0, GMT->current.proj.z_radius-s, &GMT->current.map.frame.axis[GMT_Y].item[GMT_ANNOT_UPPER+k], &tval, &label_c);
 				else if (GMT->current.proj.z_down == GMT_ZDOWN_Z) /* z = n - r */
 					ny = gmtlib_linear_array (GMT, 0.0, GMT->current.proj.z_radius-s, dy[k], GMT->current.map.frame.axis[GMT_Y].phase, &tval);
 				else if (GMT->current.proj.z_down == GMT_ZDOWN_ZP) /* z = n - r */
@@ -2926,8 +2928,8 @@ GMT_LOCAL void gmtplot_map_annotate (struct GMT_CTRL *GMT, struct PSL_CTRL *PSL,
 				}
 			}
 			else {				/* Annotate radius */
-				if (GMT->current.map.frame.axis[GMT_Y].file_custom)
-					ny = gmtlib_coordinate_array (GMT, s, n, &GMT->current.map.frame.axis[GMT_Y].item[GMT_ANNOT_UPPER], &val, &label_c);
+				if (GMT->current.map.frame.axis[GMT_Y].file_custom[k])
+					ny = gmtlib_coordinate_array(GMT, s, n, &GMT->current.map.frame.axis[GMT_Y].item[GMT_ANNOT_UPPER+k], &val, &label_c);
 				else
 					ny = gmtlib_linear_array (GMT, s, n, dy[k], GMT->current.map.frame.axis[GMT_Y].phase, &val);
 				tval = val;	/* Here they are the same thing */
@@ -9604,7 +9606,7 @@ void gmt_plotend (struct GMT_CTRL *GMT) {
 			GMT_Report (GMT->parent, GMT_MSG_WARNING, "%d extra terminations of external clip operations!\n", -GMT->current.ps.clip_level);
 		GMT->current.ps.clip_level = 0;	/* Reset to zero, so it will no longer show up in gmt.history */
 	}
-	for (i = 0; i < 3; i++) gmt_M_str_free (GMT->current.map.frame.axis[i].file_custom);
+	for (i = 0; i < 3; i++) { gmt_M_str_free(GMT->current.map.frame.axis[i].file_custom[0]); gmt_M_str_free (GMT->current.map.frame.axis[i].file_custom[1]); }
 	PSL_endplot (PSL, !K_active);
 
 	if (GMT->current.setting.run_mode == GMT_MODERN) {	/* Reset file pointer and name */
diff --git a/src/gmt_project.h b/src/gmt_project.h
index f37752f0cbc..dd05a059d4e 100644
--- a/src/gmt_project.h
+++ b/src/gmt_project.h
@@ -511,7 +511,7 @@ struct GMT_PLOT_AXIS {		/* Information for one time axis */
 	char secondary_label[GMT_LEN256];	/* Optionally use this label when axis is right or top */
 	char unit[GMT_LEN64];		/* Axis unit appended to annotations */
 	char prefix[GMT_LEN64];		/* Axis prefix starting all annotations */
-	char *file_custom;		/* File with custom annotations */
+	char *file_custom[2];	/* Files with custom annotations [0] = primary, [1] = secondary */
 };
 
 struct GMT_PLOT_FRAME {		/* Various parameters for plotting of time axis boundaries */
diff --git a/src/gmt_support.c b/src/gmt_support.c
index 6399b7d065f..f701188546a 100644
--- a/src/gmt_support.c
+++ b/src/gmt_support.c
@@ -15740,7 +15740,7 @@ unsigned int gmtlib_time_array (struct GMT_CTRL *GMT, double min, double max, st
 }
 
 /*! . */
-unsigned int gmtlib_load_custom_annot (struct GMT_CTRL *GMT, struct GMT_PLOT_AXIS *A, char item, double **xx, char ***labels) {
+unsigned int gmtlib_load_custom_annot (struct GMT_CTRL *GMT, struct GMT_PLOT_AXIS *A, char item, double **xx, char ***labels, unsigned int which) {
 	/* Reads a file with one or more records of the form
 	 * value	types	[label]
 	 * where value is the coordinate of the tickmark, types is a combination
@@ -15748,6 +15748,7 @@ unsigned int gmtlib_load_custom_annot (struct GMT_CTRL *GMT, struct GMT_PLOT_AXI
 	 * The a|i will take a label string (or sentence).
 	 * The item argument specifies which type to consider [a|i,f,g].  We return
 	 * an array with coordinates and labels, and set interval to true if applicable.
+	 * which: 0 = primary custom file, 1 = secondary custom file.
 	 */
 	int nc, error;
 	unsigned int k = 0, save_coltype, save_max_cols_to_read;
@@ -15772,8 +15773,8 @@ unsigned int gmtlib_load_custom_annot (struct GMT_CTRL *GMT, struct GMT_PLOT_AXI
 	gmt_disable_bghio_opts (GMT);	/* Do not want any -b -g -h -i -o to affect the reading from -F files */
 	GMT->current.io.max_cols_to_read = 1;
 	if ((error = GMT_Set_Columns (GMT->parent, GMT_IN, 1, GMT_COL_FIX)) != GMT_NOERROR) return (1);
-	if ((D = GMT_Read_Data (GMT->parent, GMT_IS_DATASET, GMT_IS_FILE, GMT_IS_NONE, GMT_READ_NORMAL, NULL, A->file_custom, NULL)) == NULL) {
-		GMT_Report (GMT->parent, GMT_MSG_ERROR, "Unable to open custom annotation file %s!\n", A->file_custom);
+	if ((D = GMT_Read_Data (GMT->parent, GMT_IS_DATASET, GMT_IS_FILE, GMT_IS_NONE, GMT_READ_NORMAL, NULL, A->file_custom[which], NULL)) == NULL) {
+		GMT_Report (GMT->parent, GMT_MSG_ERROR, "Unable to open custom annotation file %s!\n", A->file_custom[which]);
 		gmt_set_column_type (GMT, GMT_IN, GMT_X, save_coltype);
 		return (0);
 	}
@@ -15826,14 +15827,17 @@ unsigned int gmtlib_load_custom_annot (struct GMT_CTRL *GMT, struct GMT_PLOT_AXI
 }
 
 /*! . */
-unsigned int gmtlib_coordinate_array (struct GMT_CTRL *GMT, double min, double max, struct GMT_PLOT_AXIS_ITEM *T, double **array, char ***labels) {
+unsigned int gmtlib_coordinate_array(struct GMT_CTRL *GMT, double min, double max, struct GMT_PLOT_AXIS_ITEM *T, double **array, char ***labels) {
 	unsigned int n = 0;
 
 	if (!T->active) return (0);	/* Nothing to do */
 
-	if (T->special && GMT->current.map.frame.axis[T->parent].file_custom) {	/* Want custom intervals */
-		n = gmtlib_load_custom_annot (GMT, &GMT->current.map.frame.axis[T->parent], (char)tolower((unsigned char) T->type), array, labels);
-		return (n);
+	{	/* Determine which custom file to use: uppercase T->type means secondary (1), lowercase means primary (0) */
+		unsigned int which = isupper((unsigned char)T->type) ? 1 : 0;
+		if (T->special && GMT->current.map.frame.axis[T->parent].file_custom[which]) {	/* Want custom intervals */
+			n = gmtlib_load_custom_annot(GMT, &GMT->current.map.frame.axis[T->parent], (char)tolower((unsigned char) T->type), array, labels, which);
+			return (n);
+		}
 	}
 
 	switch (GMT->current.proj.xyz_projection[T->parent]) {
diff --git a/src/psscale.c b/src/psscale.c
index da2a5763735..2c150c8bf15 100644
--- a/src/psscale.c
+++ b/src/psscale.c
@@ -1786,7 +1786,7 @@ GMT_LOCAL void psscale_draw_colorbar (struct GMT_CTRL *GMT, struct PSSCALE_CTRL
 		}
 		if (B_set) {	/* Used -B. Must kludge by copying x-axis and scaling to y since we must use gmt_xy_axis to draw a y-axis based on x parameters. */
 			void (*tmp) (struct GMT_CTRL *, double, double *) = NULL;
-			char *custum;
+			char *custum[2];
 			double wesn_cpy[4];
 
 			A = &GMT->current.map.frame.axis[GMT_X];
@@ -1804,7 +1804,8 @@ GMT_LOCAL void psscale_draw_colorbar (struct GMT_CTRL *GMT, struct PSSCALE_CTRL
 			}
 			PSL_setorigin (PSL, 0.0, 0.0, -90.0, PSL_FWD);	/* Rotate back so we can plot y-axis */
 			/* Copy x-axis annotation and scale info to y-axis.  We don't need to undo this since gmt_end_module will restore it for us */
-			custum = GMT->current.map.frame.axis[GMT_Y].file_custom;	/* Need to remember what this was */
+			custum[0] = GMT->current.map.frame.axis[GMT_Y].file_custom[0];	/* Need to remember what this was */
+			custum[1] = GMT->current.map.frame.axis[GMT_Y].file_custom[1];
 			gmt_M_memcpy (&GMT->current.map.frame.axis[GMT_Y], &GMT->current.map.frame.axis[GMT_X], 1, struct GMT_PLOT_AXIS);
 			gmt_M_double_swap (GMT->current.proj.scale[GMT_X], GMT->current.proj.scale[GMT_Y]);
 			gmt_M_double_swap (GMT->current.proj.origin[GMT_X], GMT->current.proj.origin[GMT_Y]);
@@ -1819,7 +1820,8 @@ GMT_LOCAL void psscale_draw_colorbar (struct GMT_CTRL *GMT, struct PSSCALE_CTRL
 			gmt_xy_axis2 (GMT, -y_base, 0.0, length, start_val, stop_val, &GMT->current.map.frame.axis[GMT_Y], flip & PSSCALE_FLIP_ANNOT, GMT->current.map.frame.side[flip & PSSCALE_FLIP_ANNOT ? W_SIDE : E_SIDE] & GMT_AXIS_ANNOT, GMT->current.map.frame.side[flip & PSSCALE_FLIP_ANNOT ? W_SIDE : E_SIDE]);
 			gmt_M_memcpy (GMT->common.R.wesn, wesn_cpy, 4U, double);	/* Must temporarily switch x and y */
 			PSL_setorigin (PSL, 0.0, 0.0, 90.0, PSL_INV);	/* Rotate back to where we started in this branch */
-			GMT->current.map.frame.axis[GMT_Y].file_custom = custum;	/* Restore correct pointer */
+			GMT->current.map.frame.axis[GMT_Y].file_custom[0] = custum[0];	/* Restore correct pointers */
+			GMT->current.map.frame.axis[GMT_Y].file_custom[1] = custum[1];
 		}
 		else {	/* When no -B we annotate every CPT bound which may be non-equidistant, hence this code (i.e., we cannot fake a call to -B) */
 			if (!skip_lines) {	/* First draw gridlines */