The genetic relatedness of two kidney-parasitic Sphaerospora species was studied. Although S. renicola, the causative agent of swimbladder inflammation of common carp fingerlings (Cyprinus carpio), and Sphaerospora sp. originating from goldfish (Carassius auratus auratus) were indistinguishable on the basis of spore morphology, they were found to be genetically different as their 18S rDNA sequences shared only 71.9% identical nucleotides. In the phylogenetic trees, Sphaerospora sp. from goldfish grouped with Myxidium truttae (AJ582061) within the clade of the coelozoic freshwater species. Sphaerospora renicola clustered with S. molnari (AF378345) within the group of myxosporeans histozoic in gills. The topology of the six Sphaerospora species on the phylogenetic trees implied that myxospore morphology does not correlate with the genetic relationships, and the genus seems to be polyphyletic.