Myxozoans are a diverse group of parasitic cnidarians, with some species recognized as serious pathogens to their hosts. The present study describes 2 new myxobolid species (Myxobolus figueirae sp. nov. and Henneguya santarenensis sp. nov.) infecting skin and gill filaments of the Amazonian pimelodid fish Phractocephalus hemioliopterus, based on ultrastructural, histology and phylogenetic analysis. The fish were caught in the Amazon River, Pará, Brazil. The plasmodial development of M. figueirae sp. nov. was in the dermis and those of H. santarenensis sp. nov. were of the intralamellar type. For both species, the plasmodia were surrounded by a connective tissue layer, but there was no inflammatory infiltrate. For M. figueirae sp. nov., mature spores were ovoid measuring 9.1 to 10 (9.5 ± 0.3) µm in length, 5.8 to 6.9 (6.4 ± 0.3) µm in width and 4.4 to 4.5 (4.5 ± 0.1) µm in thickness. Two polar capsules were elongated and of unequal size. For H. santarenensis sp. nov., mature spores were ellipsoidal in the frontal view, measuring 26.3 to 36.1 (31.9 ± 3) µm in total length, 9.6 to 11.9 (10.8 ± 0.5) µm in body length, 3.7 to 4.9 (4.3 ± 0.3) µm in width and 16.6 to 25.6 (21 ± 3.1) µm in caudal process. The polar capsules were elongated and of equal size. Phylogenetic analysis, based on partial small subunit ribosomal DNA (SSU rDNA) sequences and using the closest myxozoan sequences to each one of the species studied here based on previous GenBank data, showed M. figueirae sp. nov. and H. santarenensis sp. nov. clustering in distinct lineages. While H. santarenensis sp. nov. clustered in a well-supported subclade composed of Henneguya species that infect gills of South American pimelodid hosts, M. figueirae sp. nov. clustered in a weakly supported subclade containing parasite species of bryconid hosts.