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The majority of myxosporean species (Cnidaria: Myxozoa) of the genera <i>Myxobolus</i> (35 species), <i>Henneguya</i> (8 species), and <i>Myxidium</i> (9 species) from freshwater or brackish fish in Japan were recorded more than 30 years ago (accumulatively 81.1% [43/53]). The re-discovery and molecular–genetic characterization of these species is a current research priority. During our myxosporean survey in Japanese freshwater fish, we detected three species that had never been recorded in Japan, but in the Russian Far East (Sakhalin Island, and Maritime Province): <i>Myxobolus tribolodonus</i> sp. n., forming cysts in the gills of <i>Tribolodon sachalinensis</i> (syn. <i>M. marinus</i> sensu Aseeva, 2000; <i>M. marinus</i> sensu Sokolov et Frolova, 2015, recorded from the gills of <i>Pseudaspius</i> (syn. <i>Tribolodon</i>) spp.); <i>Henneguya pungitii</i> Achmerov, 1953, forming cysts in the subcutis of external skin and buccal submucosa of <i>Pungitius sinensis</i>; and <i>Myxidium salvelini</i> Konovalov et Shulman, 1966, in the urinary bladder of <i>Oncorhynchus masou ishikawae</i>. These new isolates were characterized by integrated taxonomic approaches, i.e., myxospore morphology and molecular–genetic characterization of the small subunit ribosomal RNA gene (SSU rDNA). These new isolates were phylogenetically differentiated from any species whose SSU rDNA sequences were deposited in the DNA databases, and concurrently compared with recorded species based on classical morphological criteria. All three species were differentiated from myxosporeans previously recorded in Japan, indicating new distribution records out of the Russian Far East. For reliable species identification, accumulation of at least SSU rDNA sequences of known species worldwide is critically important.