Background Tetrahymenosis caused by about ten parasitic Tetrahymena species belonging to the Phylum Ciliophora has been recognized as an emerging problem inflicting significant economic loss in aquaculture industry in the world. Increasing knowledge and identification of Tetrahymenosis are important. Methods Four parasitic Tetrahymena species were collected from eight commercially farmed fishes in Harbin, northeastern China. Specific oligonucleotide probe and fluorescence in situ hybridization staining was designed and tested. Hoechst33342 staining methods, gene sequencing and phylogenetic analyses were also conducted. Results Tetrahymena pyriformis, T. vorax, T. chironomi and T. bergeri are the four species responsible for Tetrahymenosis in various fishes in Harbin. Taxonomy, diagnosis, diversity, pathogenicity, and histopathology of Tetrahymenosis were supplemented, analyzed and summaried, based on the present and previous work. The term Tetrahymenosis is diagnosised as diseases affecting a number of fishes, crustaceans, mollus, beetle, dragonfly, salmon, slug, midge larvae and freshwater mussel species that caused by ciliates of the genus Tetrahymena which constitutes an abundant group inhabit various aquaculture and natural habitats. Improved classification of parasitic Tetrahymena was provided. Phylogeny of parasitic Tetrahymena species was studied, and an SSU-rDNA targeted oligonucleotide probe labeled with a fluorochrome was designed, and the FISH protocol was optimized for identification of Tetrahymena species, Conclusions The manifestations of histopathology in fish typically include lesions on the body surface, and affected organs include the skin, musculature, viscera, eye socket and spinal cord; masses of ciliates can be detected in copious amount of mucus and between spaces in the damaged tissues. Improved classification of parasitic Tetrahymena is provided: facultatively parasitic forms ( T. pyriformis , T. rostrate , T. bergeri and T. vorax ), facultatively free-living forms ( T. chironomi , T. corlissi, T. rotunda, T. glochidiophila and T. papula ) and parasitic forms ( T. stegomyiae and T. limacis ).The phylogenic results indicate that Tetrahymena spp. belonging to ‘borealis’ group have a greater probability to become parasitism. the method of which can be used for quick and early detection of Tetrahymenosis.