Feasibility of assigning parentage using variable microsatellite loci was assessed for 2 species of prairie dogs. Parentage was determined from 7 microsatellite loci for 46% of juveniles born during 1994 in a colony of Gunnison's prairie dogs (Cynomys gunnisoni), and for 53% and for 45% of juveniles born during 1996 and 1997, respectively, in a colony of Utah prairie dogs (C. parvidens). Frequency of multiple paternity estimated for Gunnison's (77%) and Utah (71% and 90%) prairie dogs was greater than that detected previously for black-tailed prairie dogs (5%–10%) but within the range reported for other ground-dwelling squirrels. Of the 84 adult females and 33 adult males present during 1994 in the colony of Gunnison's prairie dogs, 75 (89%) and 22 (67%), respectively, produced weaned offspring. Breeding success for Utah prairie dogs was relatively low in 1996 (45% for females and 32% for males) but increased in 1997 (80% for females and 81% for males).