We surveyed 110 Saccostrea oysters sampled from southern Kagoshima Bay and Wakayama Prefecture to monitor the species diversity of marine benthos using morphological features and DNA barcoding. Prior to the survey, we re-identified 55 Saccostrea oysters sampled from the Yaeyama Islands, a hot spot for Saccostrea species in Japan. Analysis of partial nucleotide sequences from the mitochondrial large subunit of ribosomal DNA (LSrDNA) led to the discovery of the Indo-West Pacific rock oyster S. cucullata-F in Kagoshima Bay, and S. cucullata-C and S. cucullata-F in Wakayama Prefecture. This is the first record of the Indo-West Pacific rock oyster in mainland Japan (Hokkaido, Honshu, Shikoku and Kyushu Islands). We postulate that there may have been a northward shift in the distribution patterns of the species due to global warming, these Pacific rock oysters are relic species from the Middle or Late Pleistocene, or the non-indigenous species were introduced by oil tanker or other industrial activities.
