The myxosporean parasite Myxobolus honghuensis commonly infects farmed gibel carp (Cauratus auratus gibelio) in China. Heavy infections are associated with pop-eye, inflammation of pharyngeal wall and sever mortality in C. auratus gibelio and Carassius auratus var. red populations. In order to investigate the host range of M. honghuensis causing pharyngeal myxosporidiosis in pond cultured C. gibelio and the genetic differences among different strains, we collected a diverse range samples of C. auratus complex, including C. auratus, C. auratus var. red, C. auratus gibelio, C. auratus gibelio var. pengze, C. auratus gibelio var. qihe and C. auratus gibelio var. jinbei, a hybrid lineage of C. cuvieri (♀) and C. auratus var. red (♂), and a hybrid lineage of Cyprinus carpio (♀) and C. auratus var. red (♂). The infection prevalence of M. honghuensis in samples was determined using 18S rDNA PCR, and new ITS2 sequences of M. honghuensis were obtained through nested PCR (GenBank accession number: OR744899-OR744905). 18S rDNA PCR analysis revealed that all samples detected in this study were infected by M. honghuensis, and asymptomatic infection prevalence ranged from 25.0% to 88.2%. ITS2 sequences analysis showed only six distinct informative loci among the isolates of M. honghuensis from different fish host, and the average genetic distance was 0.003. Additionally, there were seven haplotypes identified among different isolates; H1, H2 and H3 were present only in goldfish and C. auratus var. red, while H5 was widely distributed in the samples of C. auratus gibelio of different breeds and localities. Phylogenetic analysis demonstrated that M. honghuensis isolated from C. auratus complex formed two distinct clades; notably, the strain found in goldfish displayed much closer relationship to M. ampullicapsulatus, which was commonly found on the gill of C. auratus gibelio. In conclusion, the results of this study provide crucial foundational data for understanding the epidemiology for pharyngeal myxosporidiosis in C. auratus gibelio as well as developing prevention and control strategies against the disease.