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The area occupied by colonies of the black-tailed prairie dog (Cynomys ludovicianus; BTPD henceforth) in northwestern Mexico was dramatically reduced between 1988 and 2005. We conducted a quantitative assessment of the distributional changes of these BTPD colonies during the periods 1988-2000 and 2000-2005 focusing on the potential roles of plant biomass, landscape configuration, habitat loss, and habitat suitability. We used remote sensing and GIS tools to characterize habitat and landscape conditions at areas of extinction and persistence at the beginning of each period. Based on this information, we contrasted areas of extinction and persistence within single BTPD colonies, and used logistic regression to model extinction of entire colonies. The greatest levels of reduction, fragmentation and extinction of colonies occurred between 1988 and 2000. The trend of reduction continued between 2000 and 2005 because the largest colony became smaller and fragmented, driving the area down, however, the rest of the towns showed a marginal increase. During the first period, extinction of entire colonies was higher in smaller colonies occupying low-biomass areas. Both extinction models and raw data indicate that colony area lost to agriculture and urbanization was relatively low for both periods. Because the period exhibiting the highest colony area loss coincided with a severe period of drought (1994-1995), we hypothesized that an unusually high food shortage could be the driving force behind this generalized reduction in colonies. Our results suggest that BTPD populations are sensitive to size and isolation effects mainly in the context of severe drought. Because changes in precipitation have profound impacts on plant productivity and composition in arid ecosystems, BTPD populations at the southernmost edge of their geographic range are especially vulnerable to drought and desertification processes, and therefore to climate disruption. (c) 2011 Elsevier Ltd. All rights reserved.