Infestation by parasites is a serious problem in the aquaculture industries of Micropterus salmoides Lacepède, 1802 and Ictalurus punctatus Rafinesque, 1818. Herein, Ambiphrya species are reported for the first time and cause high infestation intensity to M. salmoides and I. punctatus in China. The infestation rate of each parasite on its host was 100%, and the disease outbreaks caused 100% mortality in M. salmoides and severe histopathological lesions of gills of I. punctatus. Subsequently, we combined living observation, silver staining and scanning electron microscope to identify the Ambiphrya species. The ciliates from M. salmoides and I. punctatus were identified as Ambiphrya tholiformis Surber, 1943 and Ambiphrya ameiuri Thompson et al., 1947, respectively. Furthermore, the small ribosomal subunit (SSU) rDNA sequences of the two Ambiphrya species was obtained for the first time for further identification and phylogenetic analyses. Surprisingly, the results showed that the two Ambiphrya species formed a monophyletic clade within the family of Zoothamniidae, indicating that the genus Ambiphrya should be separated from the family Scyphidiidae. Meanwhile, A. tholiformis and A. ameiuri might be co-introduced into China along with M. salmoides and I. punctatus. Co-introduction of parasites could infest native species and cause new disease outbreaks. Therefore, more attention should be focused on detecting and monitoring the parasites of introduced fishes.