Abstract: The ciliates witch isolated from Paralichthys olivaceus in Changle, Epinephelus awoara in Fuding and Pseudosciaena crocea in Sandu′ao Ningde were identified as Cryptocaryon irritans based on morphological observation.The genomic DNA of the ciliates witch was extracted, and the gene sequence of the internal transcribed spacer 1 (ITS-1) were amplified by PCR, then cloned, sequenced and analyzed.The results revealed that the ITS1nucleotide sequence of the three strains were exactly the same.Homology comparation indicated that they shared 100%identity with the gene sequence of PYH4.12strain (DQ270010) , Wakayama strain (AB608054) , Chiayi strain (AF490381) , and shared 90.62%-99.22% identity with other sequences in NCBI database, which confirmed that the three identified strain was Cryptocaryon irritans.Furthermore, partial HSP70gene sequence was amplified from the genomic DNA of the identified Cryptocaryon irritans by PCR, and only three base pairs difference were observed in the sequence among the three strains.This indicated that the Cryptocaryon irritans Strains gotten from different hosts, different farming models in Fujian were highly homologous.