Abstract: Trichodinid ciliates are well known as ectoparasites of fishes, mollusks, amphibians, as well as crustaceans, sometimes they can cause serious diseases for the maricultured and freshwater animals. They are diverse and widely distributed in the world, and about 400 nominal Trichodina species have been reported in different environments. So far, the shortage of molecular data of trichodinids in GenBank has inhibited the development of those studies on their population genetic structure and population evolutionary history, which resulted in very little valuable information of the genetic diversity about this special group. So, in order to learn about more genetic knowledge about trichodinids, the present work was carried out. Based on the SSU rDNA sequences, the population genetic structure and genetic diversity of Trichodina reticulata Hirschman & Partsch, 1955 in China were explored. The research results of genetic structure indicated that totally nine haplotypes were detected from twenty samples, including four shared haplotypes (Hap1, Hap2, Hap3 and Hap7) and five peculiar haplotypes (Hap4, Hap5, Hap6, Hap8 and Hap9). Among them, the Hap3 from Carassius auratus was the largest shared haplotype. The Hap8 from Ctenopharyngodon idellus and Hap9 from Micropercops swinhonis were temporarily regarded as the peculiar haplotype in Wuhan and Tibet Autonomous Region, respectively. At the same time, the Hap1 from Carassius auratus was supposed to be the ancestral haplotype. Combining with the ML phylogenetic tree, Trichoina reticulata from Carassius auratus was probably the first differentiated group during the multi-host evolutionary progress, and maybe Trichoina reticulata parasitic on Ctenopharyngodon idellus was originated from Carassius auratus. The research results of genetic diversity indicated that all populations showed high haplotype diversity (H_d≥0.5) and low nucleotide diversity (P_i＜0.005), and the H_d of Carassius auratus source was significantly higher than that of Ctenopharyngodon idellus source, but the nucleotide diversity of Carassius auratus source was significantly lower than the latter. The research results of genetic differentiation (F_st) and gene flow (N_m) revealed that the group A (from Carassius auratus) and the group B (from Ctenopharyngodon idellus) were relatively independent and reached the extremely differentiated extent because of the lesser genetic communication within the group. Combining the neutral test with the nucleotide mismatch analysis, it was concluded that the group A (from Carassius auratus) has never gone through the population expansion, whereas the population expansion has probably existed during the early history of the group B (from Ctenopharyngodon idellus).