Eimerioriniid coccidia commonly infect vertebrates and might contribute to morbidity and mortality under captive conditions. The common genus Eimeria typically shows tissue specificity, usually being limited to the epithelium of the gut; disseminated infections are rare in vertebrates. Disseminated visceral coccidiosis was found in two wild-caught adult female Indo-gangetic flap-shelled turtles (Lissemys punctata andersonii) that died while in captivity at a zoo. Sporulated oocysts of Eimeria spp. were found in lung and liver of one turtle and in auditory canal, nasal mucosa, pharynx, lung, liver, kidney, spleen, and intestine of the second. Two distinct species of Eimeria were indicated for the latter case by polymerase chain reaction amplification and sequencing of a portion of the 18S rRNA gene; one species was present in nasal mucosa and liver, with a separate species in lung, spleen, and intestine. Severity of inflammation was correlated with coccidial density. Coccidia were in melanomacrophages in liver and spleen; in the interstitium of auditory canal, nasal mucosa, pharynx, lung, and intestine; and within the interstitium and epithelial cells of the renal tubules in kidney. We suggest these disseminated infections might have been facilitated by a compromised immune system.