Pharyngeal myxosporidiosis, caused by Myxobolus honghuensis, is one of the most severe parasitic diseases in the cultured allogenogynetic gibel carp, Carassius auratus gibelio (Bloch). The distribution of M. honghuensis in tissues and organs of covertly infected gibel carp was determined. Thirty 2-year-old fishes were collected from the pond, and the infection prevalence and intensity in gills, pseudobranch, spleen, liver, head kidney, middle kidney, ovary, blood, and muscle were detected via microscopic exam and quantitative PCR tests. Although the fishes did not display any obvious clinical signs, the real-time PCR tests revealed a 100% infection rate, and all fish used in this study had a covert infection of M. honghuensis. The infection prevalence of M. honghuensis in different tissues varied significantly (pseudobranch, 100%; ovary, 83.3%; gill, 73.3%; spleen, 70.0%; middle kidney, 36.7%; head kidney, 23.3%; liver, 10.0%; blood, 6.7%; and muscle, 0%). The infection intensity of M. honghuensis was inferred based on the relative expression of 18SrDNA normalized to the β-actin gene of fish host, and the real-time PCR data were analyzed using the 2^–ΔΔCt method. The infection intensity in different tissues also was signifantly different: pseudobranch, 14.4349±70.0529; ovary, 0.9556±1.5627; spleen, 0.3644±0.7854; gill, 0.3339±0.2682; head kidney, 0.2722±0.3761; middle kidney, 0.0379± 0.1055; liver, 0.0019±0.0022; and blood, 0.0012±0.0011. In conclusion, the pseudobranch of gibel carp is an important target organ in M. honghuensis infection, and should be considered as the first choice in futhre pathogen detection and disease surveillance.