Factors shaping population differentiation in low latitude seabirds are not well-understood. In this study, we examined global patterns of DNA sequence variation in the mitochondrial control region of the band-rumped storm-petrel (Oceanodroma castro), a highly pelagic seabird distributed across the sub-tropical and tropical Atlantic and Pacific Oceans. Despite previous classification as a single, monotypic species, fixed haplotype differences occurred between Atlantic and Pacific populations, and among all Pacific populations. In addition, Cape Verde and Galapagos birds formed distinct clades, estimated to have diverged from all other populations at least 150,000years ago. Azores hot season populations were also genetically distinct, lending support to previous phenotypic evidence that they be recognized as a separate species. Seasonal populations in Madeira probably represent separate genetic management units. The phylogeography of the band-rumped storm-petrel appears to have been shaped by both nonphysical barriers to gene flow and Pleistocene oceanographic conditions. Ancestral populations likely expanded through contiguous range expansion and infrequent long-distance colonization into their current breeding range. These findings suggest several possible revisions to the taxonomy of the band-rumped storm-petrel.