Sphaerospora molnari Lom, Dyková, Pavlásková and Grupcheva, 1983 often causes severe infections in the gills and skin of common carp fingerlings Cyprinus carpio carpio in Central Europe. Although most Sphaerospora spp. are coelozoic and affect the excretory system of fish, S. molnari develops mature spores in the epithelia of gill filaments, making it a rare representative of histozoic freshwater species within the genus. On the basis of a partial 18S rDNA sequence assigned as belonging to S. molnari, previous phylogenetic studies located the species within the Myxobolus clade. In the present study, S. molnari isolates from Hungary and the Czech Republic were characterized based on morphology, DNA sequence analysis and phylogenetic comparison. The obtained 3714 bp final consensus 18S rDNA sequence of the parasite showed several, sometimes extremely long inserts in the variable regions of the gene and differed considerably from the one published in GenBank in 2002. In situ hybridization confirmed the validity of the obtained DNA sequence and detected pre-sporogonic blood stages in the interstitium and blood vessels of the kidney. Phylogenetic analysis showed that S. molnari clusters within the Sphaerospora sensu stricto clade with a high support, revealing it as the first known histozoic member of the Sphaerospora subclade comprising parasites of freshwater fish.