To test the importance of special environments for local genetic subdivision in species with a larval phase, we examined allozyme variation among populations of the intertidal snail Austrocochlea constricta, in 18 tidal ponds in the Houtman Abrolhos Islands, Western Australia. Levels of genetic divergence between pond populations were correlated with those of parallel analyses among adjacent shore populations. However, divergence among the isolated ponds, which lack surface connection to the sea, were generally substantially higher, with an overall F-ST of 0.408, compared with 0.274 among the shore sites. The pond populations had less genetic variation than their shore counterparts, and the reduction of heterozygosity was correlated with the isolation of the pond population, as measured by F-ST. Both the degree of isolation and the reduction of heterozygosity were greater in deeper ponds, where snails can produce a local pool of larvae. In contrast, ponds that dry out frequently are less likely to allow production of local recruits, and these appear to be better connected genetically to adjacent shore populations. These patterns contrast sharply with those previously documented at the same sites for the direct-developing snail Bembicium vittatum, which shows greater isolation in ponds that are often dry. The comparison between the two species shows significant interaction between intrinsic and extrinsic impediments to gene flow, and highlights the importance of characteristics of the life history in determining which circumstances favour isolation of local populations.