Molecular-genetic technology and statistical methods based on principles of population genetics provide valuable information to wildlife managers. Genetic data analyzed in a hierarchical, spatial context among individuals and among populations at micro- and macro-geographic scales has been widely used to provide information on the degree of population structure and to estimate rates of dispersal. Our goals were to (1) provide an overview of spatial statistics commonly used in empirical population genetics, and (2) introduce analytical designs that can be employed to extend hypothesis-testing capabilities by incorporating space-time interactions and by using information on habitat quality, distribution, and degree of connectivity. We show that genetics data can be used to quantify the degree of habitat permeability to dispersal and to qualify the negative consequences of habitat loss. We highlight empirical examples that use information on spatial genetic structure in areas of harvest derivation for admixed migratory species, wildlife disease, and habitat equivalency analysis.