Pleistocene sea level changes substantially shaped the biogeographic patterns of co-distributed species across northern Australia. Among these species, such patterns are expected to be concordant with geomorphological transformations of the Pleistocene particularly around well-known biogeographic features. However, species-specific ecologies and life history traits may also be influential in generating patterns which depart from simple expectations. Thus, comparative population genetic studies, which use taxa that reduces variation in taxonomy and geography, may refine our understanding of how biogeographic elements shape the populations of co-occurring species. Here, we sampled Hydrophis curtus and H. elegans, two sea snake species having similar life history strategies and ecologies as well as overlapping distributions across the Torres Strait, a well-known biogeographic feature. Analyses of two mitochondrial DNA fragments and 10 microsatellite loci using traditional population genetic approaches and Bayesian clustering methods revealed that phylogeographic and population genetic patterns of these sea snake species do not align with the historical Torres Strait land bridge. Our findings contrast previous findings on closely-related Aipysurus sea snakes and may be linked to the association of Hydrophis species to soft sediment habitats. These divergent patterns between the sea snake groups present the importance of considering taxon-specific attributes in formulating conservation strategies.