The Myxobolidae family is the most diverse in the Myxozoa class and includes species that cause diseases in aquaculture and wild fish. Mapará (Hypophthalmus marginatus) is an economically important fish in the Brazilian Amazon and has been described as a host for several myxosporid taxa. In this study, the integratived the taxonomy of Alarummyxa amazonica n. sp. in a urinary bladder infection caused by H. marginatus. Myxospores have a pear-shaped to rounded body with two symmetrical polar capsules and two elliptical and flattened appendages in the posterior region, which ultrastructurally contain a valvogenic nucleus, microtubules, and glycocalyx-secreting vesicles. Phylogenetic analyses of the sequence of large and small ribosomal subunits (LSU and SSU) of rDNA indicated that A. amazonica n. sp. is part of a clade of the Myxobolidae family with histozoic freshwater fish species of the order Siluriformes. Morphological and molecular dissimilarities to other genera in the Myxobolidae family suggest the creation of a new genus that accommodates this species.