We describe three new Henneguya spp. (Myxobolidae) found parasitizing two species of cichlid fish from the Amazon basin, Brazil: H. tucunarei n. sp. from gill filaments of Cichla monoculus and H. tapajoensis n. sp. from gill filaments of Cichla pinima, both from the Tapajós River, Pará State and H. jariensis n. sp. in the fins of Cichla monoculus from the Jari River, Amapá State. We based descriptions on myxospore morphology and small subunit ribosomal DNA sequences, and used a phylogenetic analysis to compare the new Henneguya species with known relatives. Spores of the three species had similar morphology and morphometrics, but differed molecularly 5-7.5%, and were no more than 94% similar to any other sequence in GenBank. Together with having different hosts, these data supported the diagnosis of the parasites as distinct, novel species. Maximum likelihood and Bayesian analyses showed that H. tucunarei n. sp., H. tapajoensis n. sp., and H. jariensis n. sp. plus Henneguya paraensis (which parasitizes Cichla temensis) formed a well-supported sub-clade of Henneguya parasites of cichlids from the Amazon basin, in a lineage sister to those in characiforms hosts. Our analysis was consistent with previous studies that suggest that aquatic environment and vertebrate host group are the strongest correlates with phylogenetic signals in the Myxobolidae.