ABSTRACT:A set of nuclear single nucleotide polymorphisms (SNPs) and microsatellite markers was used to detect genetic stock structure among 5 Pacific green turtle Chelonia mydas nesting populations. We sampled populations in the Galapagos Islands, Ecuador (n = 57), Colola, Mexico (n = 75), French Frigate Shoals, Hawaii (n = 141), Yap, Micronesia (n = 73), and Wan-an, Taiwan (n = 57), to represent eastern, central, and western Pacific regions. A combination of 29 single independent SNPs and linked SNPs combined as haplotypes were used for a total of 20 independent markers. In addition, 8 polymorphic microsatellite markers were applied to the same sample set. Both sets of nuclear markers confirmed significant differentiation between all sampled populations in the 3 Pacific regions (p ≤ 0.001). The use of these SNPs and microsatellites resulted in sufficient power to detect small population differences not seen in previous studies using smaller numbers of nuclear markers. Our results suggest that male-mediated gene flow between regional nesting stocks is more limited than previously believed, allowing the potential to delineate stocks more clearly. Finally, we discuss the value of SNP markers as an alternative or complement to other nuclear markers such as microsatellites for the examination of stock structure.