Myxozoans are microscopic metazoan parasites which are recognized as a group of cnidarians that turned their free-living condition to parasitic life about 600 million years ago. There are more than 2 600 species of myxozoans, which mainly infect freshwater and marine fish, with a few infecting amphibians, reptiles, birds and mammals. Myxobolus Butschli 1882, with more than 900 species recorded to date, is the most speciose and widespread genus in Myxozoa, some of which can cause serious fish disease and bring great economic loss in fishery. Myxobolus miyairii Kudo 1919 is a pathogenic parasite of catfish Silurus asotus Linnaeus 1758, which is an economically important fish in China. This parasite was first discovered in Japan and subsequently found in China and Russia, successively. To investigate the strain divergence of M. miyairii from different parasitic sites and localities, the comparative study was carried out based on morphological characters, histotropism, geographic distribution, 18S rDNA sequence similarity, genetic distance and phylogeny. The myxospores of Chongqing strain 1 (infecting gill cavity membrane of S. asotus) of M. miyairii were ellipsoidal in shape with pointed anterior end and blunt posterior end. The myxospores of Chongqing strain 1 were 13.08±0.70 (10.56-13.83) μm in length and 6.09±0.55 (4.94-7.17) μm in width. The two polar capsules positioned at the anterior end of the spores, which were pyriform and equal, measured 4.97±0.39 (4.09-5.87) μm long and 1.34±0.18 (0.98-1.87) μm wide. The morphology of Chongqing strain 2 (infect intestine of S. asotus) was generally consistent with the Chongqing strain 1. The results of principal component analysis and Mann-Whitney U test on morphometry of the two strains further confirmed their morphological consistency. The similarity and genetic distance among Chongqing strain 1, Chongqing strain 2 and Jiangxi strain (infecting intestine of S. asotus) was 98.6%-99.9% and 0.000-0.013, respectively. Phylogenetic analysis showed that the Chongqing strain 2 and Jiangxi strain clustered together as a clade, which was a sister group to Chongqing strain 1. Results from sequence comparison and phylogenetic analysis indicated that M. miyairii did not form monophyletic lineages specific to geographic populations, but rather clustered according to the site of attachment; As far as the same host is concerned, different sites of attachment may have a greater impact on the population divergence of M. miyairii than that by geographic isolation. The comparative study of various strains of M. miyairii and its results are of great significance for people further understanding the evolution characteristics of M. miyairii.