We isolated and re-investigated Nephrocystidium pickii Weißenberg, 1921 (Myxozoa: Bivalvulida: Variisporina) using light microscopy and phylogenetic analysis of the small-subunit (SSU) ribosomal RNA gene. This species is a parasite of the northern pike Esox lucius L. (Actinopterygii: Esocidae) which localizes in the endothelial cells of the glomerular capillary. The results of the phylogenetic analysis including this species clarify its taxonomic status and show that although it is the closest relative to Myxidium lieberkuehni Bütschli, 1882, the two organisms are not conspecific, contrary to the earlier hypotheses. The data obtained highlight the necessity of a profound taxonomic revision of the Myxozoa and the need to clarify species affiliation of extrasporogonic developmental stages of these organisms that occur in different organs of fish.