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Fecal samples from 54 Gunnison’s prairie dogs (Cynomys gunnisoni) from Albuquerque, NM were analyzed for the presence of coccidia and all were positive. They were then relocated to an abandoned prairie dog town on the Sevilleta Long Term Ecological Research (LTER) site. Six Eimeria species, E. callospermophili, E. cynomysis, E. pseudospermophili (new host record), E. spermophili, E. ludoviciani and E. vilasi (new host record) were found in Albuquerque animals, but only two species, E. callospermophili and E. vilasi were present in relocated hosts. A significant (P < 0.05) reduction was seen in the prevalence of E. vilasi (72% vs. 13%) and in the prevalence of infections (P < 0.05) with two or more Eimeria species (39% vs. 4%) in pre- and postrelocation animals. To assess the impact of the introduction of C. gunnisoni on the resident rodent population, feces were collected from 6 species of rodents. Five Eimeria species, E. arizonensis (Reithrodontomys), E. chobotari (Dipodomys, Perognathus), E. liomysis (Dipodomys), E. mohavensis (Dipodomys) and E. reedi (Perognathus) were found. We found no evidence of coccidia transfer among introduced and resident rodent species.