diff --git a/bwamem_pair.c b/bwamem_pair.c
index 06aacff..c218925 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -301,6 +301,7 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 		h[1] = mem_reg2aln(opt, bns, pac, s[1].l_seq, s[1].seq, &a[1].a[z[1]]); h[1].mapq = q_se[1]; h[1].flag |= 0x80 | extra_flag;
 		mem_aln2sam(bns, &str, &s[0], 1, &h[0], 0, &h[1]); s[0].sam = strdup(str.s); str.l = 0;
 		mem_aln2sam(bns, &str, &s[1], 1, &h[1], 0, &h[0]); s[1].sam = str.s;
+		if (strcmp(s[0].name, s[1].name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", s[0].name, s[1].name);
 		free(h[0].cigar); free(h[1].cigar);
 	} else goto no_pairing;
 	return n;
@@ -319,6 +320,7 @@ no_pairing:
 	}
 	mem_reg2sam_se(opt, bns, pac, &s[0], &a[0], 0x41|extra_flag, &h[1]);
 	mem_reg2sam_se(opt, bns, pac, &s[1], &a[1], 0x81|extra_flag, &h[0]);
+	if (strcmp(s[0].name, s[1].name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", s[0].name, s[1].name);
 	free(h[0].cigar); free(h[1].cigar);
 	return n;
 }
diff --git a/bwape.c b/bwape.c
index 08490e7..2c96e06 100644
--- a/bwape.c
+++ b/bwape.c
@@ -706,6 +706,7 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
 			}
 			bwa_print_sam1(bns, p[0], p[1], opt.mode, opt.max_top2);
 			bwa_print_sam1(bns, p[1], p[0], opt.mode, opt.max_top2);
+			if (strcmp(p[0]->name, p[1]->name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", p[0]->name, p[1]->name);
 		}
 		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();