Abstract: This study re-described Myxobolus wulii (Wu & Li) Landsberg & Lom, 1991 and compared its strains in different sections of Yangtze River Basin (Chongqing strain, Hubei strain and Jiangsu strain) based on morphological and molecular (18S rDNA) data. The results showed that the spores and polar capsules of Chongqing strain were slightly smaller than those of Hubei strain, and that polar capsules and spores of Chongqing strain were equal in size while they were unequal for Hubei strain. The similarities and genetic distances among the three strains of M. wulii were 99.2%—99.9% and 0.002—0.007, respectively. Phylogenetic analysis showed that the sequences of M. wulii formed a poor geographical structure as well as poor host-original structure, but a strong parasitic site structure. The sequences of M. wulii clustered into two lineages: gill-parasites clade and hepatopancreas-parasites clade, indicating that the individuals of M. wulii have closer relationship with the same site of host. Moreover, the gill-parasites clade diverged earlier than hepatopancreas-parasites clade, which might be related to the evolution of external-parasites to internal-parasites. These data inferred that the gill-parasites population might be the earliest migrates of M. wulii.