diff --git a/header.c b/header.c
index d83b2b866..02283f603 100644
--- a/header.c
+++ b/header.c
@@ -1,5 +1,5 @@
 /*
-Copyright (c) 2018-2020, 2023 Genome Research Ltd.
+Copyright (c) 2018-2020, 2023, 2025 Genome Research Ltd.
 Authors: James Bonfield <jkb@sanger.ac.uk>, Valeriu Ohan <vo2@sanger.ac.uk>
 
 Redistribution and use in source and binary forms, with or without
@@ -145,7 +145,7 @@ static int sam_hrecs_update_hashes(sam_hrecs_t *hrecs,
         const char *name = NULL;
         const char *altnames = NULL;
         hts_pos_t len = -1;
-        int r;
+        int r, invLN = 0;
         khint_t k;
 
         while (tag) {
@@ -154,7 +154,11 @@ static int sam_hrecs_update_hashes(sam_hrecs_t *hrecs,
                 name = tag->str+3;
             } else if (tag->str[0] == 'L' && tag->str[1] == 'N') {
                 assert(tag->len >= 3);
+                hts_pos_t tmp = len;
                 len = strtoll(tag->str+3, NULL, 10);
+                if (tmp != -1 && tmp != len) {  //duplicate and different LN
+                    invLN = 1;
+                }
             } else if (tag->str[0] == 'A' && tag->str[1] == 'N') {
                 assert(tag->len >= 3);
                 altnames = tag->str+3;
@@ -173,6 +177,12 @@ static int sam_hrecs_update_hashes(sam_hrecs_t *hrecs,
             return -1; // LN should be present, according to spec.
         }
 
+        if (invLN) {
+            hts_log_error("Header includes @SQ line \"%s\" with multiple LN:"
+            " tag with different values.", name);
+            return -1; // LN should not be duplicated or be same
+        }
+
         // Seen already?
         k = kh_get(m_s2i, hrecs->ref_hash, name);
         if (k < kh_end(hrecs->ref_hash)) {
diff --git a/sam.c b/sam.c
index ce5833bf7..62282adcd 100644
--- a/sam.c
+++ b/sam.c
@@ -1,6 +1,6 @@
 /*  sam.c -- SAM and BAM file I/O and manipulation.
 
-    Copyright (C) 2008-2010, 2012-2024 Genome Research Ltd.
+    Copyright (C) 2008-2010, 2012-2025 Genome Research Ltd.
     Copyright (C) 2010, 2012, 2013 Broad Institute.
 
     Author: Heng Li <lh3@sanger.ac.uk>
@@ -1964,8 +1964,16 @@ static sam_hdr_t *sam_hdr_create(htsFile* fp) {
                     strncpy(sn, q, r - q);
                     q = r;
                 } else {
-                    if (strncmp(q, "LN:", 3) == 0)
-                        ln = strtoll(q + 3, (char**)&q, 10);
+                    if (strncmp(q, "LN:", 3) == 0) {
+                        hts_pos_t tmp = strtoll(q + 3, (char**)&q, 10);
+                        if (ln != -1 && ln != tmp) { //duplicate & different LN
+                            hts_log_error("Header includes @SQ line \"%s\" with"
+                                " multiple LN: tag with different values.", sn);
+                            goto error;
+                        } else {
+                            ln = tmp;
+                        }
+                    }
                 }
 
                 while (*q != '\t' && *q != '\n' && *q != '\0')