Mitochondrial DNA sequence polymorphisms and patterns of genetic diversity represent the genealogy and relative impacts of historical, geographic, and demographic events on populations. In this study, historical patterns of population dynamics and differentiation in hawksbill (Eretmochelys imbricata) and green turtles (Chelonia mydas) in the Pacific were estimated from feeding populations in the Yaeyama Islands, Japan. Phylogenetic relationships of the haplotypes indicated that hawksbill and green turtles in the Pacific probably underwent very similar patterns and processes of population dynamics over the last million years, with population subdivision during the early Pleistocene and population expansion after the last glacial maximum. These significant contemporary historical events were suggested to have been caused by climatic and sea-level fluctuations. On the other hand, comparing our results to long-term population dynamics in the Atlantic, population subdivisions during the early Pleistocene were specific to Pacific hawksbill and green turtles. Therefore, regional differences in historical population dynamics are suggested. Despite limited sampling locations, these results are the first step in estimating the historical trends in Pacific sea turtles by using phylogenetics and population genetics.