Genetic evidence of connectivity can guide the definition of effective management units and identification of barriers to gene flow. Highly vagile species are expected to exhibit high gene flow and weak population structure. However, behavioral differences may cause differentiation among groups. Black-tailed deer in northern California are partially migratory, with individuals occupying inland mountains migrating seasonally and those in low-elevation habitats occupying year-round home ranges. Greater space use by migratory deer could confer higher gene flow among them compared to that among non-migratory deer. At the same time, strong site fidelity and social affinities among deer that migrate together could genetically differentiate them from non-migratory groups. We investigated these hypotheses using microsatellite genotypes from 1,294 individuals collected throughout north-coastal California from 2015–2020. Estimated effective migration surfaces and isolation-by-resistance modeling indicated higher gene flow in the migratory than non-migratory portions of the range. However, genetic clustering analysis indicated high levels of admixture with minimal genetic differentiation between migratory and nonmigratory groups. Our findings indicate that seasonal migration increases connectivity and does not result in positive assortative mating based on behavioral differences, supporting existing management units and indicating no immediate need to address issues of genetic management among behavioral groups.