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The pathological and molecular findings associated with Histomonas meleagridis are described in a leucistic Indian peafowl (Pavo cristatus) from Southern Brazil. The most significant gross findings were multifocal necrotizing hepatitis and diphtheric typhlitis. Histopathologic evaluation of the liver, ceca, kidney, spleen, and small intestine revealed systemic histomoniasis (SH) associated with intralesional and intravascular accumulations of histomonad organisms consistent with H. meleagridis. PCR was used to amplify the DNA of H. meleagridis from the liver, ceca, small intestine, spleen, lungs, and kidneys. Direct sequencing and phylogenetic analyses confirmed that the isolate of the flagellated trichomonad identified from this investigation is more phylogenetically related to H. meleagridis than Tetratrichomonas gallinarum, Tritrichomonas foetus, and Dientamoeba fragilis. These results confirmed the occurrence of SH in this peafowl and add to the diagnosis of this disease in birds from Brazil. This report might represent the first complete identification of spontaneous histomoniasis in a peafowl due to pathological and molecular characteristics and one of the few documented cases of SH in non-commercial birds.