Human activities can change the spatial distribution of individuals within wildlife populations that in turn alters population allele frequencies and spatial genetic structure at fine scales. Artificial feeding is one such activity whose impact on wildlife physical condition, population dynamics, and transmission of disease has been well documented. To evaluate the impact of artificial feeding on the spatial distribution and social organization of white-tailed deer (Odocoileus virginianus) we estimated allele frequencies at 3 microsatellite loci for 2,177 hunter-harvested deer and characterized microgeographic genetic structure in 2 regions of the northeast lower peninsula of Michigan, USA, during and following cessation of artificial feeding. While artificial feeding was ongoing we observed no evidence of spatial genetic structure across either region. Spatial homogeneity of allele frequencies over such a large area was surprising given numerous studies that have documented spatial genetic structure in other deer populations, and it was likely a function of the aggregation of multiple kin-structured social groups (i.e., matrilines) at artificial feeding sites. Subsequently, when artificial feeding was banned, we found significant genetic differentiation among groups of deer in both regions. Detection of microgeographic genetic structure consistent with a pattern of isolation-by-distance following the ban on artificial feeding was likely the result of increased spatial segregation of social groups of related deer. Our results illustrate how analyses of the degree to which natural populations are spatially genetically structured can be used to infer the effects of human actions on wildlife movement patterns, breeding behaviors, and disease transmission that are difficult to determine using traditional methods.