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.

We collected 138 Kumamoto like oyster specimens in and around the Nakatsu tidal flat to monitor species diversity. The mitochondrial large subunit of ribosomal DNA (LSrDNA) and the nuclear ribosomal internally transcribed spacer-1 (ITS-1) region were amplified by polymerase chain reaction and restriction fragment length polymorphism analysis, leading to the discovery of the Kumamoto oyster Crassostrea sikamea in the Nakatsu tidal flat. A more accurate species identification using the nucleotide sequences for cytochrome c oxidase subunit I and ITS-1 confirmed the presence of the oysters. These results provide the first evidence of C. sikamea in the Seto Inland Sea of Japan.

The taxonomic history of members of the 37-collar-spine group within the genus Echinostoma has been very confused. We obtained DNA sequence data from the nuclear rDNA ITS1, 5·8S and ITS2 of 7 nominal species belonging to this group, Echinostoma trivolvis (Cort, 1914), E. revolution (Frölich, 1802), E. caproni Richard, 1964, E. liei Jeyarasasingam et al. 1972, E. paraensei Lie & Basch, 1967, two African isolates, E. sp.I and E. sp.II, and of one 28-collar-spined echinostome, E. hortense (Asada, 1926). Five of the eight species were clearly distinguishable using ITS data. Sequences from the remaining three taxa, E. caproni, E. sp.II and E. liei were identical to one another and the group containing these taxa was distant from other 37-collar-spine species on a phylogenetic tree. E. trivolvis and E. paraensei form a second, but less distinct group within the 37-collar-spine group. The resolution obtained using DNA sequencing will assist in the current reclassification of the group. It also provides a model for future work on sibling species.