Abstract: Trichodina nobillis Chen, 1963 is an ectoparasitic ciliate for freshwater fishes, distinguished by its unique fan-shaped blade. While previously recorded from different hosts including fishes, amphibians, and crustaceans, it occurs predominantly on Cyprinidae fishes. The host named as Tinca tinca belonging to the Leuciscinae Cyprinidae of economic importance, has been poorly studied with regard to parasitic diseases, especially the Trichodiniasis. Although T. nobillis is a common and important pathogen in aquiculture, population-related research is extremely scarce. To explore intraspecific differentiation and phylogenetic relationships of T. nobillis, specimens were collected from the gills of cultured Tinca tinca in Yongchuan, Chongqing (CQ population) and Meishan, Sichuan (SC population). Based on the newly obtained morphological data and SSU rDNA sequences, we compared the population difference of T. nobillis and clarified its interspecific relationships with related species. Morphologically, the denticle morphology of adhesive disc was highly consistent between the two populations, but the SC population exhibited more developed denticles, whereas the CQ population lacked a distinct posterior projection. The quantitative analysis revealed significant differences (P<0.05) in denticle span, ray length, number of radial pins, and denticular ring ratio. The PCA analysis further supported the existence of intraspecific variation. Molecular phylogenetic analysis based on SSU rDNA showed lower sequence similarity and greater genetic distance between T. nobillis populations from the same host than among those from different hosts, suggesting that host differences were not the primary driver of genetic differentiation. Parasitological assessment indicated that T. nobillis is an epibiotic trichodinid with no strict host or site specificity, reflecting a broad ecological niche as a non-obligate parasite. This study reports T. tinca was established as a new host record for T. nobillis. Molecular evidence also helped clarify the taxonomic distinction between T. nobillis and the closely related Trichodina heterodentata (GenBank accession: AY788099). These findings provide a taxonomic foundation for future studies on T. nobillis and related species, as well as theoretical insights for the prevention and control of trichodinid diseases in aquaculture.