Waldrapp ibis (Geronticus eremita) are a critically endangered species, and there are currently more birds in captivity than in the wild. A juvenile, male Waldrapp ibis housed in a mixed-species exhibit was found dead with no premonitory signs. Necropsy revealed extensive necrotizing hepatitis associated with numerous pleomorphic protozoa that were immunohistochemically reactive with antibodies raised against Tritrichomonas foetus, a parasite of cattle. Electron microscopy confirmed the organisms as members of family Trichomonadidae, and sequence analysis of the first ribosomal internal transcribed spacer region (ITS1), 5.8S ribosomal RNA, and ITS2 regions indicated high genetic similarity (96-97%) to members of the Tetratrichomonas gallinarum complex. The animal was born in captivity, and no introductions in this exhibit had occurred since 2009. Other Waldrapp ibis that had contact with the infected male were negative for flagellate infections by fecal examination, thus cross-species transmission is proposed as the source of infection. The host range of the T. gallinarum complex is very large and although the pathogenicity of its members, especially for wild birds, is controversial, these parasites should be considered as a possible cause of acute mortality in Waldrapp ibis. In addition, immunohistochemistry with T. foetus antibodies and molecular diagnostics may be useful tools for preventative veterinary care of endangered bird populations. A greater understanding of the ecology and pathogenesis of this pathogen may also be vital for screening subclinical captive populations and existing wild populations prior to reintroduction efforts.