Mapping the distribution of genetic diversity of species over their geographic range is crucial from a conservation perspective. We investigated nesting populations of an iconic and endangered species, Chelonia mydas, the green sea turtle, in French Polynesia. Sequences of the mtDNA control region of 97 specimens were analyzed using Bayesian phylogeny reconstruction, Bayesian dating, and skyline plots. Samples from French Polynesia belonged to four of the nine recognized Indo-Pacific lineages, with two lineages (III and IV) recognized as widespread and two other lineages (V and VI) geographically restricted to the South Pacific. More than half of the specimens belonged to the geographically restricted lineages, and suggested the existence of two South Pacific refugia during glacial periods, a western one (represented by lineage V) and an eastern one (represented by lineage VI), herein revealed from French Polynesia. Expansions of populations were recovered in most of the lineages and were all dated after the Last Glacial Maximum, similarly to the Atlantic populations of C. mydas. Finally, as the likely existence of a glacial refugium near French Polynesia matches a previously published predicted refugium under future climatic conditions, this makes the area particularly promising for the conservation of green sea turtle populations.