Wildlife managers are challenged to manage spatially structured populations efficiently and effectively, therefore dispersal and gene flow are vital to understand and manage, particularly for a harvested species. We used a genetic approach to describe the metapopulation structure of Rocky Mountain elk (Cervus elaphus) in Idaho to assess past patterns of population distribution and influences of harvest. We used elk tissue and DNA samples (n = 216) to examine genetic dissimilarity between 7 regions and 9 elk management zones throughout Idaho using microsatellite loci (n = 11). Using 5 approaches, including pairwise F_ST-values, assignment tests, and a Bayesian model–based clustering of genotypes, we examined the distribution of genetic variation. The distribution of genetic variation between elk populations indicated low levels of genetic differentiation among regions (expected heterozygosity [H_E] = 0.55–0.61, overall F_ST = 0.011) and elk management zones (H_E = 0.54–0.60, overall F_ST = 0.017). Assignment tests and migration rates indicated directional gene flow between elk populations. A patchy metapopulation best describes the distribution of genetic variation among Idaho elk populations because likely enough individual interchange occurs between geographically separated populations. The elk populations we sampled could be part of a geographically larger patchy metapopulation potentially stretching from Yellowstone National Park through Idaho into western Canada. Because of historical translocations of elk from Yellowstone National Park, insufficient time may have passed to detect differences in genetic variation. Subtle differences in the distribution of genetic variation were observed in 2 of the 9 elk management zones within 2 different regions of the state. Our findings indicate management of Idaho elk populations and dispersal are maintaining sufficient gene flow. Metapopulation structure of a harvested species based on the distribution of genetic variation is an indicator of potential genetic consequences of harvesting and sustainable harvest levels.