The yellow-bellied sea snake, Pelamis platurus (Elapidae, Hydrophiinae), has the largest distribution of any snake species, and patterns related to its distribution and regional color variation suggest there is population structuring in this species. Here, we use mitochondrial (ND4, Cyt-b) and nuclear (RAG-1) DNA to (1) test whether genetic variation is associated with local variation in color pattern, and (2) assess whether large-scale patterns of genetic variation are correlated with geographic distribution across the Pacific Ocean. We found low levels of genetic variation and shallow population structure that are correlated with local variation in color pattern and with geographic distribution. The low levels of genetic divergence indicate a relatively high rate of gene flow throughout the Pacific region and/or a recent expansion of range, both of which could be attributable to the passive drifting of these snakes on oceanic surface currents. The mtDNA data conform closely to a model of past exponential population growth, and this may have been associated with the species' large eastward and westward expansion of range. The pattern of low nucleotide and high haplotype diversity suggests that this population growth occurred in the relatively recent past. Data from drifting buoys can potentially act as informative models for predicting patterns of drifting in Pelamis and for generating additional testable hypotheses relating to its population structure and biogeography. Future studies should employ nuclear microsatellite markers to investigate population structure in this species at a finer scale. The exploitation of oceanic currents as a novel and highly efficient dispersal mechanism has likely facilitated gene flow throughout the Pacific Ocean in this uniquely pelagic species of sea snake, resulting in a distribution spanning over half of the earth's circumference.