Myxozoa are microscopic parasites that principally infect fish. Some species can cause serious fish disease leading to great economic losses. Thelohanellus kitauei is one of those pathogenic species found in many areas. To clarify the genetic variation and phylogenetic relationships among different geographic strains of T. kitauei. Comparative analyses were conducted on strains of T. kitauei from Chongqing of China, Hubei of China, Shioda of Japan, Jeonbuk of Korea and Seoul of Korea based on their morphology. The comparison and analyses were also conducted for their site variation, similarity, genetic distance, genotype and phylogeny based on 18S rDNA sequences. The morphological characteristics of strains of T. kitauei from different localities were generally consistent. Among different strains, the similarities were 99.5%-100.0%, variation sites were 0-6, genetic distances were 0.000-0.004, based on 18S rDNA sequences. The phylogenetic analysis showed that thelohanellids with membrane sheath clustered as a clade and the remaining thelohanellids without membrane sheath clustered as another clade. The clade without membrane sheath was divided into fin-infection group and gill-infection group. The membrane sheath should not be used as a valid feature for species identification of T. kitauei whose identification should still be according to its morphology and morphometry of the spore excluding membrane sheath. Though the shape and size of membrane sheath was unstable, its presence or absence on thelohanellids might associate with phylogeny of thelohanellids. And the evolution pattern for clade possessing membrane sheath might be different from the clade without membrane sheath. The strains of T. kitauei did not form special differentiation in different parasitic sites and also did not form monophylies in different localities. The reason for this genetic situation might be: the isolation time was not long enough or there was the high frequence of gene flow among different strains which led to limited population differentiation.