The pharyngeal myxosporidiosis caused by Myxobolus honghuensis is one of the most severe parasitic diseases in the culture of Carassius auratus gibelio. In order to reveal the tissue distribution and differences of M. honghuensis in the diseased and asymptomatic C. auratus gibelio. This study has collected and examined the muscle, pseudobranch, gills, head kidney and other 11 organs by microscopic, one-tube semi-nest PCR and histopathological section. Microscopical exam showed that the sporocyst and mature spores were most detected in the pharynx, pseudobranch and gills of diseased fish，while the mature spores were enclosed with yellow nodal and most detected from pseudobranch and first efferent branchial artery in the asymptomatic gibel carp. PCR results showed M. honghuensis could be detected in most of the tested organs in diseased fish except muscle，and pseudobranch had the highest infection rate (100%). In asymptomatic C. auratus gibelio, positive results were detected in pharynx, pseudobranch, head kidney, kidney, spleen and ovary，and the highest infection rate (26.7%) also was from the pseudobranch. Tissue sections of the diseased C. auratus gibelio showed M. honghuensis forming numbers of sporocysts between the pharynx wall and skull，and some near the pharyngobranchials. The pseudobranch was seriously destructed by the sporscysts, and the sporogonic cells of M. honghuensis could be observed near the left pseudobranch filament. Based on the microscopic exam and PCR test, this study firstly found that the pseudobranch may be the main parasitic and sporogonic site of M. honghuensis, and revealed the infection variation of M. honghuensis between the diseased and asymptomatic C. auratus gibelio.