Black-tailed prairie dog (Cynomys ludovicianus) is an influential species in prairie ecosystems. Accurate estimates of active prairie dog colony area are needed to assess the status of the species and evaluate the effects of management actions. In 2008, Montana Fish, Wildlife and Parks conducted a survey of potential black-tailed prairie dog habitat. Using fixed-wing aircraft and an aerial line-intercept method, we surveyed 771 transects totaling 56,530 km in 32 counties in central and eastern Montana, USA, excluding tribal lands. We recorded 667 black-tailed prairie dog colony intercepts totaling 336,636 m in 21 counties. Ground intercepts were 1.091 (95% credible intervals = 1.087–1.094) times longer than air intercepts. The estimated percent of colonies classified as active from the air that were active on the ground was 86.8% (95% credible intervals = 77.9–93.5%). Corrected estimates resulted in 77,430 ha (95% credible intervals = 69,480–83,380) of active and 12,990 ha (95% credible intervals = 7,039–20,970) of inactive black-tailed prairie dog colonies. We conducted a sensitivity analysis of the estimated area of active prairie dog colonies by reducing a percentage of long intercepts assumed to be entirely active. More than 30% of active intercepts >750 m in length would need to, in fact, be inactive in order for our active colony area estimates to differ >10,000 ha (13%; i.e., outside of our margin of error) from our estimates. Aerial line-intercept methods provide a reliable and repeatable method for obtaining estimates of active and inactive prairie dog colony area over large areas. Our estimates provide the basis for long-term monitoring of prairie dogs on a landscape scale. © 2013 The Wildlife Society.