Temporal genetic variation was examined in a coyote (Canis latrans) population that experienced intensive removal for several decades. The population experienced separate periods of nonselective and selective control, and comparisons were made between control methods. Analyses at 11 microsatellite loci revealed only subtle genetic differences between removal regimes when analyzed by year of birth or resident status. Numbers of alleles per locus (4–16) and expected heterozygosities (0.617–0.915) were high across groups and few 1st-order relatives were detected within groups. Coyote social structure and dispersal patterns appear to adequately maintain genetic variation and promote genetic homogeneity over relatively small geographic scales during periods of locally aggressive removal.