Black-tailed prairie dogs (Cynomys ludovicianus) currently live in metapopulations in the parts of their range where plague, caused by the bacterium Yesinia pestis, has invaded. Prairie dogs are highly susceptible to the pathogen, with most animals within towns dying during Y. pestis outbreaks. A review of population genetic studies of prairie dogs demonstrates considerable differentiation between prairie dog towns. Despite declines and fluctuations in size of prairie dog populations, they continue to harbor considerable genetic variation. This results from continual dispersal and gene flow, likely along low-lying drainages that connect towns. When combined with estimates of population size, the landscape genetic approach described here will provide precise estimates of dispersal and gene flow, in addition to evaluation of long-term stability of prairie dog metapopulations.