We examined the ocean-wide genetic population structure of Pacific cod (Gadus macrocephalus) using electrophoretically detectable population markers at 41 protein loci. Samples were collected at 11 locations extending over most of the species's range from the Yellow Sea, Korea, to Puget Sound, Washington. Seven loci (17%) were polymorphic using the 0.05 criterion of polymorphism. Sample heterozygosities ranged from 0.018 to 0.041 and averaged 0.025 (±0.013). Two major genetic groups were detected: a western North Pacific Ocean (Asian) group and an eastern North Pacific group (including Bering Sea stocks). The UPGMA Nei genetic distance, D, (based on 41 loci) between samples from these two groups was 0.025, and this subdivision accounted for 18.9% of the total gene diversity. Genetic differentiation between these two groups appears to reflect the barrier effects of coastal Pleistocene glaciation. Morphological and tagging data from other studies suggest that Pacific cod are subdivided into several independent stocks. In this study, significant allele-frequency differences were detected between samples within the eastern North Pacific Ocean, the Bering Sea, and the western North Pacific Ocean, but not between stocks on a larger geographic scale. The average Nei genetic distance (based on 41 loci) between samples was only 0.0007, and a gene diversity analysis indicated that within-region differences represented only 3.1% of the total gene diversity. There was a slightly greater amount of differentiation between the Yellow Sea and the Sea of Japan (D = 0.0041), which reflects geographic isolation of the Yellow Sea stock not found in other areas. From theoretical considerations, little genetic divergence between stocks of Pacific Cod is expected because random genetic drift in large population sizes is insignificant and because migration between areas prevents genetic differentiation.