The present study consists of a detailed phylogenetic analysis of myxosporeans of the Myxobolus and Henneguya genera, including sequences from 12 Myxobolus/Henneguya species, parasites of South American pimelodids, bryconids and characids. Maximum likelihood and maximum parsimony analyses, based on 18 S rDNA gene sequences, showed that the strongest evolutionary signal is the phylogenetic affinity of the fish hosts, with clustering mainly occurring according to the order and/or family of the host. Of the 12 South American species studied here, six are newly described infecting fish from the Brazilian Pantanal wetland. Henneguya maculosus n. sp. and Myxobolus flavus n. sp. were found infecting both Pseudoplatystoma corruscans and Pseudoplatystoma reticulatum; Myxobolus aureus n. sp. and Myxobolus pantanalis n. sp. were observed parasitizing Salminus brasiliensis and Myxobolus umidus n. sp. and Myxobolus piraputangae n. sp. were detected infecting Brycon hilarii.