A new genus and species of the gastropod family Capulidae, Vermeijia japonica, is described from the upper Pliocene Kuwae Formation in Niigata Prefecture and the lowermost part of the Sasaoka Formation in Akita Prefecture, Japan. This genus is similar to the boreal genus Ariadnaria although it was collected in association with several warm-water species. In another gastropod family, Nassariidae, Cyllene satoi is a new species from the upper Pliocene Tentokuji Formation in Akita Prefecture. Nine warm-water taxa in the Omma-Manganji fauna, including Cyllene, no longer live in the Japan Sea, except for its westernmost part. They suggest that the Tsushima Current had a higher SST during the late Pliocene than at present. Vermeijia is the fourth extinct genus of the Omma-Manganji fauna, but it disappeared in the Japan Sea by Datum A (2.75 Ma), earlier than the other three genera, which became extinct by the end of the early Pleistocene.