Myxozoans are common microscopic endoparasites in fish, and some are highly pathogenic to their wild and farmed fish hosts. In the present study, myxosporeans infection in the kidney of silver carp Hypophthalmichthys molitrix (Valenciennes, 1844) from Lake Taihu, was investigated, and two dominate species, Myxobolus lieni (Nie & Li, 1973) and M. varius (Achmerov, 1960), with infection prevalence 60.2% and 35.2%, respectively, were well characterized based on morphological, histopathological and DNA sequence data. M. lieni formed small roundish plasmodia in the epithelial cells of renal tubules. The mature myxospores appeared suborbicular, slightly flat in frontal view and fusiform shaped in sutural view. Dispersed myxospores of M. varius were found in the renal interstitium without forming plasmodia structures and enclosed within melano-macrophage centers. The spore appeared elliptical in frontal view, with wider anterior than posterior and shuttle shaped in sutural view. Interestingly, the occurrence of myxozoans in the kidney detected with SSU rDNA PCR and clone sequencing, revealed co-infection of five Myxobolus species. BLASTn search indicated SSU rDNA gene sequences obtained here were not identical to any sequence available in GenBank. Phylogenetic analyses showed that the five Myxobolus species detected here were clustered together, forming a separate clade of cyprinid-infecting myxozoans.