The invertebrate animals endemic to deep-sea hydrothermal vents are distributed intermittently along relatively linear oceanic ridge axes. A one-dimensional stepping-stone model, therefore, provides a reasonable starting hypothesis of population structure for these species. Nevertheless, population genetic studies of many species from eastern Pacific vents did not detect the expected signatures of isolation-by-distance (IBD). Instead, distinct patterns of geographical subdivision have been attributed to the unique dispersal modes of individual species, topographical discontinuities of the ridge axes, nonequilibrium metapopulation scenarios and cryptic species. Here, we reexamined these inferences in light of expectations generated by computer simulations of a one-dimensional stepping-stone model. We evaluated whether the previously inferred subdivisions are statistically robust to an alternative explanation that continuous stepping-stone migration has occurred along the ridge axes but discontinuities in the sampling design (gaps) have generated the apparent disjunctions. We found that previous inferences about barriers to gene flow (vicariance) were supported in many cases, but that failures to detect evidence for IBD could be explained by low statistical power associated with the sampling effort. The simulation approaches presented here might be useful for testing the significance of inferred phylogeographic gaps in other species.