In order to identify the pathogen which caused mass mortality in farmed Cyprinus carpio var. specularis in Deyang district of Sichuan Province, China, the pathogen of this event was determined following bacteriology, parasite morphological observation, histopathology and PCR detection. The results showed that bacteriological examination was negative whereas parasite was positive with Thelohanellus kitauei. Histologically, intestinal damage is the most serious, where a large number of parasitoid cysts were noted. Morphological observation showed that the total length and width of the spores were about 23–30 μm and 10–15 μm, respectively. In addition, the polar capsule was 11–15 μm long and ovalellipsoidal, which accounted for about 1/3–1/2 of spores. The outer layer of the spores covered with a thin colorless and transparent film. One pyriform macronucleus was in the upper part and two globular micronuclei near the iodinophilous vacuole. Tissue DNA from infected intestine was identified as T. kitauei (TKF-1) by nest polymerase chain reaction amplification of the 18S SSUrRNA gene and the sequenced 18S SSUrRNA gene of TKF-1 has a homology up to 100% with T. kitauei in GenBank. According to the results we confirmed that the death of C. carpio var. specularis in this region was caused by T. kitauei.