Myxobolus miyairii Kudo, 1919 was first reported from the intestines of the Amur catfish (Silurus asotus) in Japan and then in China and Russia, but with incomplete description. During the investigation of fish myxosporean diversity in Poyang Lake, the biggest lake along the Yangtze River, China, two Amur catfish highly infected with M. miyairii in the intestine wall were sampled. So, the complete description of this species with morphological and molecular data was presented here. A large number of whitish, round or ellipsoidal pseudocysts 0.32-0.78 mm in diameter could be found in the external intestinal wall after dissecting the infected fish. Mature spores of M. miyairii were elongated and ellipsoidal in the frontal view and narrow fusiform in the lateral view, with a slightly pointed anterior end and a bluntly rounded posterior end and measured 13.3 ± 0.49 (12.5-14.7) μm × 6.6 ± 0.27 (6.2-7.4) μm × 5.0 ± 0.26 (4.4-5.7) μm in size. Spore surface was smooth and two spore valves symmetrical, with a thin and straight sutural ridge. Interestingly, two types of caudal appendage (single or bifurcated) were occasionally present on the posterior end of some spores which has not previously been reported. The two equal pyriform polar capsules measured 6.5 ± 0.30 (6.2-7.5) μm long and 1.9 ± 0.14 (1.5-2.3) μm wide and situated at the anterior end of the spore. Polar filaments coiled with eight to nine turns, perpendicularly to the longitudinal axis of the polar capsules. Histopathological analysis showed that the plasmodium developed in the circular muscle layer of intestinal wall of Amur catfish, but no obvious inflammatory responses were observed. Phylogenetic analysis based on the partial 18S small subunit ribosomal DNA sequences indicates that M. miyairii cluster within a clade of Siluriforme-infecting Henneguya species with the support of a high bootstrap value, but also evolutionarily independent from the Henneguya clade infecting the epithelium of fish of the Ictaluridae family. Additionally, Myxobolus species reported with caudal processes dispersed within the Henneguya-Myxobolus clade.