Genetic markers are often used to designate population units for management and conservation, but widespread sharing of mitochondrial DNA control-region haplotypes defined from short (< 500 base-pair [bp]) sequences often limits inferences of population connectivity in marine turtles. Haplotype CM-A8, defined from 490-bp sequences, dominated the haplotype profiles of the 3 major green turtle (Chelonia mydas) rookeries in Brazil. Previous analyses based on 490-bp haplotypes did not detect differentiation between the northern rookeries of Atol das Rocas and Fernando de Norohna, but did indicate differentiation of the northern rookeries from Trindade Island in the south. We reexamined the stock structure of the Brazilian green turtle rookeries using 817-bp control region and mitochondrial short tandem repeat (mtSTR) sequences. Nine 490-bp haplotypes were subdivided into 41 haplotypes by combining 817-bp and mtSTR sequences. Eight of the 14 CM-A8 turtles from Fernando de Noronha carried mtSTR haplotypes that were not detected in the larger rookeries. Pairwise exact tests indicated that the northern Brazilian green turtle rookeries of the Rocas Atoll and Fernando de Noronha are discrete populations with respect to female natal homing. Moreover, several apparently endemic markers in the 3 Brazilian green turtle nesting populations should improve resolution of future mixed-stock analyses. Comparable data are needed from green turtle rookeries in the central and eastern Atlantic to assess structure and connectivity at the ocean basin scale.