Abstract
The I ndo‐ A ustralian archipelago ( IAA ) supports the world's highest diversity of marine fish, invertebrates and reptiles. Many of the marine fish and invertebrates show congruent phylogeographic patterns, supporting a view that the region's complex geo‐climatic history has played an important role in generating its exceptional biodiversity. Here, we examine population genetic structure of the viviparous sea snake, H ydrophis curtus , to assess how past and present barriers to gene flow in the IAA have contributed to genetic and species diversity in a fully marine reptile. Mitochondrial and anonymous nuclear sequences and ten microsatellite loci were used to identify patterns of historical genetic structure and population expansion, reconstruct dated genealogies and assess levels of recent gene flow. These markers revealed strong concordant geographic structure within H . curtus with a prominent genetic break between populations broadly distributed in the I ndian O cean and the W est P acific. These populations were estimated to have diverged in the late P liocene or early P leistocene, and microsatellite admixture analyses suggested limited recent gene flow between them despite the current lack of barriers to dispersal, indicating possible cryptic species. Subsequent divergence in the mid–late Pleistocene was detected within the W est P acific clade among the populations in the P huket‐ T hailand region, S outh‐ E ast A sia and A ustralia, and two of these populations also showed genetic signals of recent range expansions. Our results show that climatic fluctuations during the P lio‐ P leistocene generated high levels of cryptic genetic diversity in H . curtus , and add to similar findings for diverse other marine groups in the IAA .