diff --git a/jcvi/graphics/karyotype.py b/jcvi/graphics/karyotype.py
index 0ce97d43..42bcb634 100644
--- a/jcvi/graphics/karyotype.py
+++ b/jcvi/graphics/karyotype.py
@@ -361,7 +361,8 @@ def __init__(
         di = lambda x: x[:-1] if x[-1] == "-" else x
         # Comments can cause layout and seqids to be out of sync
         # https://github.com/tanghaibao/jcvi/issues/676
-        for i, row in enumerate(_ for _ in fp if not _.startswith("#")):
+        for i, row in enumerate(_ for _ in fp if not _.startswith("#") and _.strip()):
+            logger.info("Processing `%s` (track %d)", row.strip(), i)
             t = layout[i]
             # There can be comments in seqids file:
             # https://github.com/tanghaibao/jcvi/issues/335
diff --git a/tests/graphics/data/seqids_with_empty_lines b/tests/graphics/data/seqids_with_empty_lines
new file mode 100644
index 00000000..29ee8e3f
--- /dev/null
+++ b/tests/graphics/data/seqids_with_empty_lines
@@ -0,0 +1,6 @@
+
+
+chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19
+
+Pp01,Pp02,Pp03,Pp04,Pp05,Pp06,Pp07,Pp08
+
diff --git a/tests/graphics/test_karyotype.py b/tests/graphics/test_karyotype.py
index 78b5a6cb..15b13e41 100644
--- a/tests/graphics/test_karyotype.py
+++ b/tests/graphics/test_karyotype.py
@@ -36,4 +36,8 @@ def test_main():
         ["seqids_with_comments", "layout", "-o", "karyotype_with_comments.pdf"]
     )
     assert op.exists(image_name)
+    cleanup("karyotype_with_empty_lines.pdf")
+    image_name = karyotype_main(
+        ["seqids_with_empty_lines", "layout", "-o", "karyotype_with_empty_lines.pdf"]
+    )
     os.chdir(cwd)