An understanding of habitat selection is important for management of wildlife species. Although bobcat (Lynx rufus) resource selection has been addressed in many regions of the United States, little work has been conducted in the Northern Great Plains. From 2006–2008 we captured and radiocollared 20 bobcats in the Badlands (n = 10) and Black Hills (n = 10) regions of South Dakota. During the summers of 2008 and 2009 we collected habitat measurements at 349 (176 Badlands, 176 Black Hills) bobcat locations and 321 (148 Badlands, 173 Black Hills) random sites. Microhabitat characteristics at bobcat use sites varied with region (P < 0.001) and sex of bobcat (P < 0.001). Percent slope, shrub, low cover, medium cover, and total cover were greater (P ≤ 0.017) at bobcat locations in the Black Hills than in the Badlands whereas distance to drainage was greater (P < 0.001) at locations in the Badlands than in the Black Hills. In the Badlands, male bobcat locations were closer (P ≤ 0.002) to prairie dog towns and drainages and had greater (P < 0.05) percent forbs and forb height than random sites, whereas females were closer to badland formations (P < 0.001) than random sites. In the Black Hills, male locations were at greater elevation (P < 0.001) and female locations were characterized by greater (P ≤ 0.02) grass height, shrub height, low cover, and total cover than random sites. Logistic regression indicated that microhabitat selection was similar between study areas; odds ratios indicated that odds of bobcat use increased by 0.998 (95% CI = 0.997–0.999) per 1 m increase in distance to drainage, 0.986 (95% CI = 0.978–0.993) per 1.0% increase in grass cover, by 1.024 (95% CI = 1.011–1.036) per 1 cm increase in grass height, by 1.013 (95% CI = 1.003–1.024) per 1% increase in forb cover, and by 1.028 (95% CI = 1.017–1.039) per 1% increase in medium cover. Our results were similar to other bobcat microhabitat selection studies, where bobcat relocations were associated with understory vegetation, drainages, and rugged terrain. These results identify the adaptability of the species to meet life history requirements in a variety of landscapes, and provide insight to how land use requirements vary within regional and management boundaries.