Abstract
A recently published complete mitochondrial genome of Japanese or Temminck's cormorant (Phalacrocorax capillatus) was the first of this species (GenBank accession number LC714913). Comparison of COI sequences shows that this mitogenome clustered with great cormorant (Phalacrocorax carbo) rather than with its sister taxon P. capillatus. This suggests that the mitogenome was either a misidentified P. carbo or represents previously unknown intraspecific diversity in P. capillatus overlapping with that of P. carbo. Unfortunately, no voucher specimen was retained so it remains impossible to distinguish between these alternatives. We suggest that great restraint should be exercised using this mitogenome as a reference for P. capillatus. We reiterate previous pleas to retain voucher specimens for mitogenome sequences to enable re-analysis of the identity of the material.