This study provides morphological and molecular data of a new parasite species found in the muscle layer of the intestinal tract of the South American silver catfish, Rhamdia quelen from Marajó Island region (Pará State, Brazil), an important fishery resource with recognized potential for fish farming. The morphology of these parasites was reanalyzed and phylogenetic analyses were run on their 18S rDNA gene sequences. The spores were morphologically distinct from those of other Myxobolus species described previously. The obtained partial sequence of the 18S rDNA gene sequences of the new species were compared to those of 24 other Myxobolus and Henneguya species available in GenBank. The results of morphological and molecular analyses indicated clearly the existence of a new species, Myxobolus marajoensis sp. n.