Both physical and non-physical barriers can restrict gene flow among seabird populations. Understanding the relative importance of non-physical barriers, such as breeding phenology, is key to understanding seabird biodiversity. We investigated drivers of diversification in the Leach’s storm-petrel species complex (Hydrobates spp.) by examining population genetic structure across its range. Variation in the mitochondrial control region and six microsatellite loci was assayed in birds sampled from breeding colonies throughout the North Atlantic and North Pacific (H. leucorhoa leucorhoa), as well as from San Benito Islands (H. l. chapmani), and two seasonal populations in Guadalupe (summer breeding H. socorroensis and winter breeding H. cheimomnestes), Mexico. Weak but significant differentiation was found between populations of H. l. leucorhoa breeding in the Atlantic versus North Pacific, as well as between H. l. chapmani and H. l. leucorhoa, and between H. socorroensis and H. cheimomnestes within Guadalupe. In contrast, strong differentiation in both mitochondrial DNA and microsatellites was found between H. leucorhoa and both H. socorroensis and H. cheimomnestes. Phylogenetic reconstruction suggested the Guadalupe seasonal breeding populations are sister taxa, at least in their mitochondrial DNA. Non-physical barriers to gene flow appear to be more important than physical barriers in driving divergence within the Leach’s storm-petrel species complex. In particular, allochronic speciation may have occurred between the seasonal populations within Guadalupe. Further work should include higher resolution sequencing to confirm results, and an increased sampling effort, particularly within the California area, to fully resolve the relationship between H. l. leucorhoa and H. l. chapmani.