In January 2003, fecal samples from 13 live pygmy rabbits, Brachylagus idahoensis (Merriam, 1891), were collected at the Oregon Zoo in Portland, Oregon, and sent to the University of New Mexico (UNM), Albuquerque, New Mexico, to be examined for coccidia. In July 2004, 14 more fecal samples were collected and sent to UNM, 6 from some of the same rabbits and 8 from 16 other rabbits (4 were pooled samples from siblings). In addition, tissue sections from 3 dead rabbits (2 from the Oregon Zoo, 1 from Washington State University) also were examined. Two of 4 (50%) pooled fecal samples and 8 of 17 (47%) 1-rabbit samples were positive for a single species of Eimeria, which we describe here as a new species. Sporulated oocysts were subspheroidal, 25.6 × 23.8 (22–28 × 21–27) μm, with a length:width (L:W) ratio of 1.1 (1.0–1.2). A micropyle (∼2 μm wide) and 0–1 polar granules were present, but an oocyst residuum was absent. Sporocysts were ellipsoidal, 13.4 × 8.1 (11– 16.5 × 7.5–9) μm, with a L:W ratio of 1.7 (1.3–2.2), and they had a Stieda body and sporocyst residuum. Tissue sections showed a heavy infection of the villous epithelial cells of the proximal and mid-small intestine with coccidial endogenous stages, but no stages were found in liver hepatocytes. Meronts with approximately 46 (26–70) merozoites per infected cell appeared to be fully developed and were subspheroidal, 14.8 × 13.9 (13–18 × 10.5–16.5) μm. Developing macro- and microgamonts were indistinguishable from each other and were spheroidal to subspheroidal, 10.4 × 9.5 (9–11 × 7.5–10.5) μm. Mature macrogamonts were spheroidal to subspheroidal, 14.2 × 13.7 (12–17 × 11–16) μm, and mature microgamonts were smaller and subspheroidal, 11.9 × 10.8 (10.5–13 × 9–12) μm. This eimerian seems to be extremely pathogenic to young pygmy rabbits, and given the precarious nature of this unique genetic population, it appears to be an emerging pathogen that deserves immediate further study.