Mitochondrial DNA (mtDNA) sequences were determined for 168 green turtles (Chelonia mydas) nesting at the 3 known rookeries in Brazil: Trindade (n = 99), Atol das Rocas (n = 37), and Fernando de Noronha (n = 16). In addition, 32 green turtles were sampled on foraging grounds at Atol das Rocas and Fernando de Noronha. Significant genetic structure exists among the 3 rookeries, with haplotype frequencies significantly different between Trindade and the other 2 rookeries, and no significant difference between Atol das Rocas and Fernando de Noronha. In contrast to previous reports, we found no significant relationship between population size and mtDNA diversity when 14 Atlantic green turtle rookeries were compared for 3 measures of diversity. There was also no significant relation between rookery latitude and mtDNA diversity. Our results are consistent with the earlier hypothesis that haplotype CM-A8 is the closest relative to an ancestral Atlantic haplotype and the observation that CM-A8 is the most common and widespread haplotype in equatorial rookeries. Bayesian and hierarchical mixed stock models yielded similar estimates of rookery contributions to the Atol das Rocas and Fernando de Noronha foraging aggregation, with Ascension Island the primary source and with probable contributions from the Greater Caribbean and West Africa. This study provides data from the southwest Atlantic that are critical for an Atlantic-wide analysis of green turtle population structure.