Abstract: During the diseases monitoring of goldfish in Fuzhou area, a kind of myxospore was found in the pharynx of goldfish Carassius auratus. In order to identify the parasite, 18S rDNA and ITS-5.8S gene of the Myxosporean were amplified by PCR, while the sequences of the two genes were used to construct the phylogenetic tree for further analysis, respectively. The results showed that the morphology of the myxospore was similar to that of Myxobolus honghuensis, and the sequence identity of 18S rDNA gene was 98.08 % between them. Besides, the specific primers of ITS-5.8S gene for the identification of M. honghuensis were succeed in amplifing the target gene of the myxospore. Combined with the parasitic parts, morphology as well as phylogenetic analysis, the myxospore could be identified as M. honghuensis. The findings were the first report of an infection of M. honghuensis in the pharynx of goldfish besides C. auratus gibelio, and of great benefit to the understanding of the hosts and parasitic parts. In addition, this work provided references with the early diagnosis of diseases of the pharynx-parasitising myxobolus.