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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. This study expanded on previous work supporting differentiation between eastern and western populations using mtDNA and utilized a panel of 13 microsatellite loci to provide additional insight into the population structure of gray whales. Comparison of microsatellite allele frequencies indicated that eastern and western populations are genetically distinct. Although highly statistically significant, the level of nuclear differentiation between the two populations was relatively low, and the results of sex-specific analyses and assignment testing suggested that some degree of male- biased dispersal may occur between populations. Within the set of samples collected from animals on the primary western feeding ground, relatedness analyses revealed that, consistent with field observations, the fidelity of females and their offspring to this area have been important in shaping the structure of the population. Furthermore, analysis of the paternity of animals first identified as calves, with known and sampled mothers, in the western population between 1995 and 2007 identified 18 males as putative fathers, providing evidence that many of the animals identified on the Sakhalin feeding ground interbreed with each other, presumably while sharing a common migratory route. However, the success of the paternity assignment was lower than expected given the high proportion of sampled animals in this population, suggesting that some males which are contributing to reproduction may not use the primary western feeding ground on a regular basis. The combination of these results suggests that the population structure of gray whales in the North Pacific is more complex than previously thought, and that some movements between the eastern and western populations may take place. However, 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