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Within the North Pacific, gray whales (Eschrichtius robustus) are recognized as distinct eastern and western populations. Although both populations were severely reduced by whaling, the eastern population is generally considered to have recovered while the western population has remained highly depleted. Previous studies have documented genetic differentiation between the two populations on the basis of mtDNA haplotype frequencies. Since mtDNA represents only maternal inheritance patterns, the present study used bi-parentally inherited microsatellite markers (n=13) to measure differentiation between populations as well as to compare levels of nuclear genetic diversity retained in each. Mean levels of genetic diversity, as measured by the microsatellites, were similar between the eastern and western populations, indicating that the western population has retained relatively high levels of nuclear genetic diversity despite its small size. Comparison of microsatellite allele frequencies confirmed that eastern and western populations are genetically distinct. Although highly statistically significant, the level of differentiation between the two populations is relatively low, and sex-specific analyses suggest that some amount of male-biased dispersal may occur between populations. While these results suggest some movements between the eastern and western populations may take place, the maintenance of genetic differences between the two populations supports their recognition as separate eastern and western populations. Future efforts should focus on elucidating the nature and extent of any dispersal which is occurring in order to better understand factors potentially influencing the recovery of the small western population.