Testing theories of dispersal is challenging in highly migratory species. In sea turtles, population size, geographic distance, natal homing, and ocean currents are hypothesized to affect dispersal. Little is known, however, about these mechanisms in sea turtles foraging along the South American coast. Green sea turtles feeding at Ubatuba (UB, n = 114) and Almofala (AF, n = 117), Brazil, were sequenced at the mitochondrial DNA (mtDNA) control region (486 bp) and genotyped at 7 microsatellite loci to test dispersal hypotheses. Fifteen mtDNA haplotypes were revealed, including a previously undescribed sequence, and the average observed heterozygosity (H(o)) was 76.4%. Overall short-term temporal differences were not detected, and differentiation was less pronounced in microsatellite than in mtDNA analyses. Mitochondrial results reveal significant differentiation between the Brazilian feeding grounds and most other Atlantic groups, whereas microsatellites uncover similarities to some of the geographically closest populations. Ubatuba and Almofala are mixed stocks, drawn primarily from Ascension, with lesser contributions from Surinam/Aves and Trindade. Costa Rica is also a significant source of individuals feeding at AF. The results are consistent with a model of juvenile natal homing impacted by other factors. Effective protection of turtles foraging along the extensive Brazilian coast may enhance breeding populations thousands of kilometers away.