Black-tailed prairie dogs (Cynomys ludovicianus) are a species of concern and accurate estimates of occupied area are required to assess their status. We conducted aerial line-intercept surveys to estimate colony areas in Colorado, USA, 2006–2007. Optimal allocation based on results from a previous (2002) survey was used to distribute flight time to sample 28 counties. Uncorrected estimates of active and inactive colony areas from the aerial surveys were 329,529 (SE = 16,841) ha and 18,292 (SE = 2,366) ha, respectively. We attempted to ground-truth a randomly selected sample of 186 colony intercepts but gained complete access to only 150. Ground-truthing demonstrated that aerial surveys estimated only 96% of the true lengths of colony intercepts but overestimated the proportion of active colonies. Corrected estimates of active and inactive colony areas are 319,165 (SE = 20,105) ha and 42,422 (SE = 11,485) ha, respectively. Because ground-truthing was not conducted in the original 2002 survey, uncorrected estimates from this survey are the appropriate metric to be used for comparison to the 2002 data. Our estimates demonstrated a 29% increase (SE = 6.3) in area occupied since surveys were conducted in 2002. These results are useful to state and federal agencies and other conservation partners in determining the condition of the species when conducting status reviews.