Partial 18S rDNA sequences of five myxosporean species, Myxobolus rotundus, M. rotundatus, Thelohanellus wuhanensis, Henneguya weishanensis and M. cubanicum were amplified utilizing two common primers myxoF (5'-CGCGGTAATTCCAGCTCCAGTAG-3') and myxoR (5'-ACCAGGTAAGTTTTCCCGTGTTGA-3') and stored in the GenBank with the access number AY165179-AY165183. By combining the 18S rDNA sequences of other 13 species available in the GenBank a parsimonious tree of 18 species was built with Polypodium hydriforme used as the outgroup. Results show Tetracapsula bryozoides and "PKX" organism lie on the root within the Myxozoa before the divergence of other major groups which form two clades as T. wuhanensis-T. hovorkai-M. rotundatus-M. rotundus-M. bibullatus-M. pellicides-M. pendula-H. salminicola and H. exilis-H. ictaluri-M. spinacurvatura-M. osburni-H. lesteri-H. weishanensis-M. kubanicum. Among the genus myxobolus, 3 species found in China did not form a Glade but grouped with the European species, indicating that the geographic divergence of Myxobolus may not be distinct. Neither Myxobolus nor Henneguya was monophyletic and these two genera can not be distinguished using the molecular data. It is further proposed that the caudal protrusion of Henneguya may not be a valid taxonomic character but an appending structure homologous with the "V" projections in Myxobolus.