Isospora gopheri n. sp. (Apicomplexa: Eimeriidae) is described from 5 of 28 (18%) Morafka's desert tortoise Gopherus morafkai Murphy, Berry, Edwards, Leviton, Lathrop & Readle, housed by the Phoenix Herpetological Society, Maricopa County, Arizona, USA. Sporulated oöcysts of this new species were spheroidal to subspheroidal, 20-27 × 19-27 (23.0 × 21.7) µm, with a smooth, bi-layered wall and 1-3 polar granules; an oöcyst residuum was absent. Sporocysts were elongate-ovoidal to ellipsoidal, 13-18 × 9-12 (15.9 × 10.2) µm, with a Stieda body, sub-Stieda body and sporocyst residuum; sporozoites were banana-shaped with an ellipsoidal posterior refractile body and a spheroidal anterior refractile body. This is both the first coccidian to be described from this host species and only the second reported from the host genus.