Dispersal and nesting philopatry are two processes that affect the connectivity, evolution, and long-term viability of populations, and thus have important conservation implications for threatened and endangered species. Here we investigate dispersal, relatedness, and the fine-scale spatial genetic structure of Eastern Box Turtles (Terrapene carolina carolina) at the northern extreme of their geographic range in northwestern Michigan. We analyzed georeferenced microsatellite genotypes (n = 165) using global, sex-specific, and two-dimensional local spatial autocorrelation (2D LSA), as well as spatial principal components analysis (sPCA). Genetic diversity was low relative to Eastern Box Turtle populations in the middle of the range. We found dispersal was male-biased, as only females showed significant positive spatial genetic autocorrelation at distances less than 2 km. 2D LSA showed local genetic “hotspots” of related turtles that tended to correspond with known nesting areas. We found evidence for global genetic structure using sPCA, which we attribute to genetic clustering rather than clinal variation. Our results suggest that restricted female dispersal and fidelity to limited open-canopy nest sites result in fine-scale spatial genetic structuring in this population. We stress the importance of maintaining high quality nesting habitat and habitat corridors for transient males, which appear to be critical for functional connectivity of Eastern Box Turtles.