The Sicydiinae subfamily (Teleostei: Gobioidei) is a diverse group of fish found in tropical insular river systems in the Indo-Pacific area, the Caribbean region and West Africa. They spawn in freshwater and their larvae drift downstream to the sea where they develop, before returning to rivers to grow and reproduce (amphidromous). The geographic distribution patterns of Sicydiinae species are variable and can range from endemic to widely spread across several oceans. Knowledge of how and from where species have emerged to occupy their current geographic ranges is essential for understanding evolution of the group and for developing strategies for their conservation. Phylogenetic studies show that evolutionary history has played a major role in determining species’ distribution patterns, but more recent events and dispersal also appear to have shaped present distribution and connectivity patterns of Sicydiinae species in the Indo-Pacific region. We assessed past and present genetic structure of populations of two species that are widely distributed in theCentralWest Pacific and which have similar pelagic larval durations. Spatial analyses of genetic variation in Sicyopus zosterophorum demonstrated strong isolation across the Torres Strait, which was a geologically intermittent land barrier linking Australia to Papua New Guinea. However, this geographical barrier did not seem to affect Smilosicyopus fehlmanni. Historical, demographic and ecological hypotheses need to be tested to explain the different patterns of population structure and distribution between these species. Our findings suggest that strategies to conserve amphidromous fish should consider the presence of cryptic evolutionary lineages to prevent stock depletion.