Freshwater gastropods often have limited dispersal capability and small geographic ranges, and face severe threats from habitat loss and degradation. However, in addition to the scarcity of knowledge on their life history traits, species taxonomy has not been adequately resolved and boundaries between intra- and interspecific variation remain unclear for many taxa. One such example of an indeterminate species boundary with implications for conservation issues is the relationship between the thiarid snails Stenomelania crenulata in Okinawa and southwards (ranked as CR EN in the 2012 Japanese Red List) and S. rufescens in mainland Japan (VU). The results of our multi-disciplinary investigation into variation in the shell morphology and mitochondrial (COI) and nuclear (ITS-1) gene sequences suggest that S. rufescens represents a geographic variant and a junior synonym of S. crenulata. The widespread geographic range of S. crenulata, spanning a few thousand kilometers north to south, is possible due to an amphidromous life cycle that involves a marine planktotrophic larval phase and upstream migration after settlement in estuaries. Nevertheless, there is recognizable morphological and genetic differentiation between distant populations, probably reflecting a relatively short pelagic duration and possibly also infrequent transoceanic dispersal; metamorphic competence is achieved in two weeks in full seawater and even more rapidly in brackish water. The Okinawan population, with only a few known localities, therefore deserves the high conservation priority; conservation efforts need to involve the proper maintenance of migration pathways including all marine, brackish and freshwater environments.