Areas occupied by white-tailed prairie dogs (WTPD; Cynomys leucurus) and Gunnison's prairie dogs (GPD; C. gunnisoni) are not well-known in Colorado (USA) and elsewhere. Suitable methodology for monitoring changes in populations of WTPD and GPD over broad areas also has not been well established. We evaluated occupancy modeling methodology to establish baseline occupancy rates for WTPD and GPD in Colorado. We estimated that WTPD occupied 24.1% (SE = 12.8) of 47,710 0.25-km² plots and GPD occupied 7.5% (SE = 1.3) of 158,225 0.25-km² plots in Colorado during 2004 and 2005. Areas reported as colonies in the Colorado Division of Wildlife's database were not good predictors of WTPD and GPD occupancy. Occupancy rates were highest for GPD at intermediate elevations. We estimated detection probabilities for surveys from the ground of 0.760 (SE = 0.042) for WTPD and 0.786 (SE = 0.060) for GPD. Probability of detection for WTPD improved with lower temperature and earlier Julian date, whereas no covariates improved detection rates for GPD. We recommend that wildlife managers use occupancy monitoring to establish status and trends in populations of WTPD and GPD across their range.