The renal parasite Eimeria auritusi has caused several mortality events in double-crested cormorants (DCC; Phalacrocorax auritus) in the Midwest and southeastern United States. This parasite has only been detected during large-scale outbreaks, and its presence and prevalence in healthy populations of cormorants is unknown. In this study, 80 DCC were collected from the Chattahoochee River near Fort Gaines, Georgia, and examined for kidney and intestinal coccidia. Eighteen (22.5%) and 56 (70%) of the DCC were positive for E. auritusi and a new species of intestinal Eimeria, respectively. Oocysts of the new intestinal Eimeria species had a thin colorless wall, were ovoid with rare bumps on the outer surface, and measured 17.1 μm ± 1.5 × 14.7 μm ± 1.0 (16–18.5 × 13–17), with an average length:width ratio of 1.17 μm (1.03–1.29). A prominent micropyle (4–4.5 μm) was present, and a large oval-to-round polar body (2.5 μm) was located beneath the micropyle. Sporocysts were ovoid and measured 9.6 μm ± 0.6 × 5.9 μm ± 0.5 (8.5–10.5 × 5–6.5), with an average length:width ratio of 1.63 (1.3–1.82) with small stieda body present. Amplification and sequencing of a fragment of the 18S rRNA gene indicated that the 2 DCC Eimeria species and 2 Eimeria species from cranes were in a separate group from other Eimeriidae. These data indicate that E. auritusi and this new species of intestinal Eimeria are prevalent in this apparently healthy DCC population. The cause of renal coccidiosis outbreaks in other populations of cormorants is unknown but could be due to crowding or stress during the winter months or some other associated pathogen or immunosuppressor that might predispose individuals to clinical disease.