Aim Historical patterns of ocean circulation in the Southern Hemisphere have been well studied, but the effects of coastal oceanography on marine biogeography in this region remain poorly understood relative to northern latitudes. Our study investigates historical and contemporary patterns of migration and dispersal across the Tasman Sea. Location Coastal regions of the Tasman Sea including southeastern Australia, Tasmania and New Zealand. Taxon Hippocampus abdominalis, the pot-bellied seahorse, one of the most broadly distributed seahorse species, and the only seahorse to have successfully colonized New Zealand from Australia across 2,000 km of open ocean. Methods We used a multilocus genetic dataset to measure population diversity and differentiation from seahorses across the full species range to investigate contemporary and historical demography, and to reconstruct colonization routes across the Tasman Sea. Results Genetic data indicate that seahorses colonized New Zealand from Australia during the previous interglacial-glacial cycle (12,000-120,000 ybp), and have evolved in relative isolation since the initial establishment event. Contemporary effective population sizes in the newly colonized range are substantially larger than those inferred in Australia, and both appear to be reduced relative to ancestral levels. Australian seahorses are genetically diverse and show high levels of population connectivity, while the distribution of genetic variation in New Zealand suggests an initial colonization of the South Island following by northward migration. Importantly, despite clear evidence that New Zealand seahorses are descendent from Australian ancestors, patterns of contemporary genetic diversity are consistent with trans-Tasman migration from New Zealand to Australia, suggesting that genetic variation accumulated in the newly colonized range is contributing to the genetic diversity of Australian seahorses. Main conclusions Despite a largely independent evolutionary trajectory of seahorses separated by the Tasman Sea, haplotype sharing between populations in Australia and New Zealand suggests that secondary genetic exchange is contributing to the contemporary phylogeography of the species. Patterns of genetic structure in H. abdominalis mirror those found in other rafting species, suggesting that adult dispersal via rafting has been an important vector of marine dispersal in this species.