Melampus “sincaporensis,” Auriculastra “duplicata”, and Ellobium chinense are Red-Listed snail species of the family Ellobiidae that co-occur on salt marshes in mainland Japan. Here, we report the genetic diversity and population structures of the former two taxa in comparison with our previous data on E. chinense for the evaluation of connectivity and conservation values of their local populations. Analyses of 655-bp or 652-bp sequences of the mitochondrial cytochrome c oxidase subunit I gene showed the highest genetic diversity and panmictic structure for M. sp. cf. sincaporensis throughout its geographic range in Japan, whereas they showed the highest level of genetic subdivision for A. sp. cf. duplicata. Our laboratory observation of egg masses and planktotrophic larvae of A. “duplicata” and reference to previous ontogenetic data for the species of Melampus suggested differences in their fecundity and pelagic larval duration, which apparently have led to the contrasting levels of population differentiation in the study species. Particular need of conservation efforts was identified for the isolated population of A. “duplicata” in the Ise–Mikawa Bay area to avoid local extinction and shrinking of the species' geographic range. In addition, we present molecular and morphological evidence that individuals of A. “duplicata” from mangrove swamps in the northern part of Okinawa Island represent an independent, surviving lineage of a different species.