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Genetic depletion is one of the main problems associated with biodiversity loss affecting the adaptation and survival of populations and species to rapidly changing conditions. In this contribution, we approximate expected loss of genetic variation in black-tailed prairie dog (Cynomys ludovicianus) colonies from the Janos Biosphere Reserve (northern Chihuahua, Mexico) after a bottleneck experienced by this population in 2013. For this purpose, we used 10 nuclear microsatellite loci to estimate the effective population size (Ne) and modelled the expected effects of a severe bottleneck on genetic diversity (expected heterozygosity, HE). Also, we attempted to prioritize their conservation value by using genetic (mitochondrial cytochrome b andcontrol region plus nuclear microsatellite loci) and ecological data (colony area and relative density). Our analyses indicate that additional data should be gathered for a more precise estimation of prioritization and extinction indexes. In addition, continuous monitoring should be implemented for early detection of population declines and prevention of further losses of genetic diversity. We indicated the colonies that are more likely to lose genetic diversity and should be targets for restoration and management efforts. Inglés