We assessed the geographic distribution of the Mexican prairie dog (Cynomys mexicanus) by comparing historical reports, data from a 1996 study, and our distribution estimations from 1999. We located 54 active and 22 inactive prairie dog colonies, determined size for each one, and evaluated whether colony size and isolation had an impact on the persistence of colonies and likelihood for recovery. We estimated a current total distribution of 322 km² within the Mexican states of Nuevo León (234 km²), Coahuila (82 km²), and San Luis Potosí (6 km²). The occupied range of the Mexican prairie dog suffered a 33% reduction from 1996 to 1999 and an overall reduction of 74% when compared with its documented historical range. We found no relationship between isolation and colony size for active colonies, although geographic isolation can result in decreases in the chances of colonies surviving stochastic events. Other challenges for the recovery of this species include the increased rate of habitat loss and deterioration, and landscape desertification factors.