Myxobolus including 979 species, is the largest genus in Myxozoa, which can parasitize different tissues in fish and bring about myxosporosis to result in various degrees of economic losses in the fishery. To identify the pathogen infecting the gill of common carp and analyze the pathogeny of its gill seriously damaged, those methods on morphometry, molecular biology, phylogeny and histopathology were employed in the research. The results showed that the myxospore of the pathogen was elliptic or nearly round in valvular view, lemon shape in sutural view, olive shaped in apical view. The myxospore was 9.2-11.8 μm long, 8.3-10.5 μm wide and 4.4 μm thick. Two water-drop polar capsules were unequal in size. The anterior ends of the two polar capsules were slightly close together. The larger polar capsule was 3.5-4.7 μm long and 2.4-3.1 μm wide, while the smaller one was 2.8-3.8 μm long and 1.8-2.6 μm wide. Polar filaments within the large and small polar capsules were coiled with 5 and 3 turns, respectively. V-shaped folds were obvious in the posteriors of some spores. However, intercapsular appendix as well as mucous envelope and aiodinophilous vacuole was not observed. The similarity of 18S rDNA between M. basilamellaris reported and the present species was 99.69%. Thus, morphological and molecular data of the parasite as well as host species proved that the present species is M. basilamellaris, and this is a new record in China. The cysts developed between the afferent and efferent arteries of the diseased carp’s gills. Due to the increase of cyst volume, the afferent and efferent arteries were compressed to be deformed and blocked, and the bases of filaments were also mechanically fractured. Some connective tissues around the cysts were destroyed. Moreover, the myxospores infiltrated into the surrounding tissues after the rupture of the cysts. Therefore, the main cause of death for diseased carp is that the cysts of M. basilamellaris oppressed the main vessels and fractured the gills, which resulted in poor blood flow and insufficient blood supply, and finally led to the loss of respiratory function of gills. The morphological, molecular and pathological data on M. basilamellaris from this study can provide a theoretical basis for its prevention and control in aquaculture.