Analyses of mitochondrial (mt) DNA control region sequences from 175 leatherback turtles Dermochelys coriacea from 10 nesting colonies revealed shallow phylogenetic structuring of maternal lineages on a global scale. Eleven haplotypes were observed, and mean estimated sequence divergence, p = 0.00581, is much lower than the deepest nodes reported in global mtDNA surveys of the green turtle Chelonia mydas, loggerhead Caretta caretta, and ridley turtles Lepidochelys spp. The leatherback turtle is the product of an evolutionary trajectory originating at least 100 million years ago, yet the intraspecific phylogeny recorded in mitochondrial lineages may trace back less than 900 000 years. The gene genealogy and global distribution of mtDNA haplotypes indicate that leatherbacks may have radiated from a narrow refugium, possibly in the Indian–Pacific during the early Pleistocene glaciation. Analysis of haplotype frequencies revealed that nesting populations are strongly subdivided globally (FST = 0.415), and within ocean basins (FST = 0.203–0.253), despite the leatherback's highly migratory nature. Within the Atlantic significant differences in haplotype frequency distributions and Nm values < 2 are observed in pairwise comparisons between St. Croix (U.S. Virgin Islands) and mainland Caribbean populations, and between Trinidad and the same mainland populations. These findings provisionally support the natal homing hypothesis for leatherback turtles, although several proximal nesting populations were indistinguishable, suggesting recent colonization or less precise natal homing behaviour than documented for other marine turtle species. The evidence of natal homing, manifested on ecological time scales, may be erased in some populations by rapid rookery turnover resulting from climatic fluctuation and the ephemeral nature of nesting habitat on a geological time scale. The evolutionary effective population size (Ne) is estimated from mtDNA data to be between 45 000 and 60 000, a value that exceeds current global census estimates of 26 000 to 43 000 adult females.