Within the Northern Bighorn Basin, Wyoming, prairie dog (Cynomys) survey data collected between 1980 and 1989 were compared with data from a 2001–2005 survey. From these data, distribution, activity level, and habitat selection based on range site and precipitation categories were analyzed. Overall, the white-tailed prairie dog (C. leucurus) population declined in distribution and activity. Occupied active area decreased 71 percent from 7,031.8 ha (17,374.9 ac) to 2,011.5 ha (4,970.6 ac); there was also a 37 percent decrease in active town abundance and a 55 percent decrease in the mean active town area. Declines in occupied area for the Meeteetse Metapopulation (87 percent) were greater than declines for the remaining population (Basin Metapopulation - 39 percent). There was also a very small population of black- tailed prairie dogs (C. ludovicianus) that increased 8 percent to 77.4 ha (191.3 ac). Density of active burrows declined significantly (P < 0.006) for the Basin Metapopulation. The mean nearest neighbor distances separating white-tailed prairie dog towns for both surveys were approximately 2.0 km. Towns appear to be significantly associated with saline upland, loamy, sandy, shallow loamy, and shale range sites (P < 0.0001). White-tailed prairie dogs were also significantly associated with precipitation zones (P < 0.0001) and may prefer the 20.3–25.4 cm (8–10 in) precipitation zone even though they were more common in the 12.7–22.9 cm (5–9 in) precipitation zone. Other variables not measured also likely contribute to the observed distribution of white-tailed prairie dog town site selection.