In this study, published Holocene ostracod data for Osaka, Hiroshima, and Iyo-nada Bays within the Seto Inland Sea (SIS), Japan, are re-examined. Five major faunal changes are recognized at different stratigraphic horizons (Horizons 1–5) in the Holocene sedimentary record. Horizons 1 and 5 (faunal changes) were most likely triggered by the respective openings of the Bisan-seto (and resulting formation of the SIS) and Akashi Straits. Three other major faunal changes, at Horizons 2–4, may also be linked to the opening of straits and resulting formation of bays, although the exact nature of these events is less certain. This re-examination indicates that the opening of straits extensively affected the benthic inner-bay community during the Holocene transgression in the SIS. Further high-resolution studies are needed for confirmation of faunal changes triggered by opening of straits.