The geographic range of sea kraits encompasses one of the geologically most-complex regions of the world. At its center lies Wallacea (the transition between the terrestrial biotas of the Asian and Australian tectonic plates) and the Indonesian Throughflow (nexus of the equatorial marine biotas of the Indian and Pacific oceans). The aim of this study was to elucidate the role of paleogeography, paleoclimatology, and oceanic currents in the evolution and distribution of sea kraits across these major biogeographic crossroads and beyond. A recent assessment of times of taxonomic divergence was projected against paleogeographic reconstructions to produce a parsimonious, hypothetical model of events critical for the origin, dispersal, and differentiation of this taxon. Times and degree of divergence of taxa suggested by recent morphological and molecular studies are in accord with various climatological and geologic events. The model postulates that the distribution of sea kraits was neither greatly affected by tectonics, other than the approach of the Australian Plate to the Asian one, nor dominated by the historic barriers to dispersal of terrestrial fauna across Wallacea, or by the Indonesian Throughflow. Rather, the model suggests that two major factors—paleogeographic alteration of the configuration of land and sea, and the directions of sea currents, past and present—provide an explanation of how these amphibious snakes (1) originated from a terrestrial Asian elapid ancestor, (2) subsequently generated the venomous Australian land snakes and their derivatives the true sea snakes, and (3) differentiated into the species complexes, species, and infraspecific entities of the genus Laticauda.