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Phylogenetic trees based on parabasalid sequences of the small subunit rRNA placed Histomonas meleagridis in close proximity to Dientamoeba fragilis, Tritrichomonas foetus, and Monocercomonas sp. In this study, we sequenced partial genes of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), enolase, and alpha-tubulin from 2 strains of H. meleagridis. We found 5 different GAPDH sequences, 6 different enolase sequences, and 3 alpha-tubulin sequences. Phylogenetic trees based on the obtained sequences showed a close relationship of H. meleagridis with T. foetus and, to some extent, Monocercomonas sp. In conclusion, our findings further corroborate the ssu rRNA-based tree. Consequently, our study also supports the hypothesis that H. meleagridis secondarily lost cytoskeletal structures.