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Background  Myxozoans are metazoan parasites whose traditional spore morphology-based taxonomy conflicts DNA based phylogenies. Freshwater species of the genus  Hoferellus  are parasites of the excretory system, with several members infecting food and ornamental fish species, as well as amphibians. This study aims to increase our understanding of their molecular diversity and development, aspects about which little is known, and to generate a molecular diagnostic tool to discriminate between different pathogenic and non-pathogenic  Hoferellus  spp.    Methods  SSU and ITS rDNA phylogeny, along with morphological descriptions using light and electron microscopy were used to identify and characterize  Hoferellus  species collected from the urinary system of fishes and frogs. A PCR-based diagnostic assay was designed to differentiate between cryptic  Hoferellus  spp in cyprinid fishes commonly cultured in Central Europe.    Results  Our phylogenetic results separate the species of  Hoferellus  into two phylogenetic sublineages which are indistinguishable on the basis of generic morphological traits: 1) The  Hoferellus sensu stricto  sublineage, which is composed of the type species  Hoferellus cyprini ,  Hoferellus carassii  and a cryptic species,  Hoferellus  sp. detected only molecularly in common carp. 2) The  Hoferellus sensu lato  sublineage into which the new species we described in this study,  Hoferellus gnathonemi  sp. n. from the kidney of the elephantnose fish and  Hoferellus anurae  from reed frogs, are placed together with  Hoferellus gilsoni  previously sequenced from European eel. Apart from phylogenetic analyses, we also provide novel ultrastructural data on the phagocytotic nature of some  Hoferellus  plasmodia and on the elusive intracellular stages ascribed to the presporogonic development of this genus.    Conclusions  We provide molecular evidence of the polyphyly of the genus  Hoferellus  and provide novel morphological details of its members. Based on the presented data, we revise and propose emendation of the genus  Hoferellus .

Species complexes and phylogenetic lineages of Hoferellus (Myxozoa, Cnidaria) including revision of the genus: A problematic case for taxonomy