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The use of molecular techniques for the assessment of familial relationships among social species of mammals has become relatively commonplace. However, some species represent poor candidates for such studies due to naturally low levels of genetic diversity, leading to unacceptably large standard errors associated with estimates of relatedness. Here, we report on a preliminary study of genetic diversity within two populations of a social species of ground squirrel, Gunnison's prairie dog (Cynomys gunnisoni) using DNA fingerprinting. We observed low levels of diversity in the form of large mean coefficients of genetic similarity among individuals occupying the same population. Overall similarity, determined from the combined data, yielded by three minisatellte probes, ranged from 55 to 61%. These values place Gunnison's prairie dog at the extreme upper end of the range of similarity values reported for outbred species of mammals (ca. 0.20-0.50). As a partial means of explaining these results, and as a means of comparing our results to those of similar studies using allozymes, we determined the level of differentiation between our two study colonies in the form of an F-statistic analog. A value of 0.11 (± 2.26 × 10−3) was obtained and is similar to values reported from allozyme studies (0.07–0.12). A significance test of this value yielded a positive result (D = 5.63, d.f. = 1, P < 0.025), demonstrating that gene flow between populations is limited, a factor that may help to maintain low levels of diversity.