Abstract: To supplement molecular data of Chloromyxum ellipticum and elucidate its intraspecific genetic variation, this study conducted morphological observations and multi-gene rDNA molecular phylogenetic analyses on positive samples isolated from the gallbladders of 81 cultured grass carp (Ctenopharyngodon idellus) from five districts (Hechuan, Dazu, Jiangjin, Changshou, and Wanzhou). Morphological observation recorded 10—16surface striations, 4—5 polar filament coils, a myxospore length of 7.58±0.64 (6.26—9.83) μm, a myxospore width of 6.02±1.08 (5.36—7.99) μm, a polar capsule length of 2.29±0.25(1.38—2.79) μm, and a polar capsule width of 1.35±0.26(0.93—1.55) μm. Phylogenetic, haplotype, principal component, and genetic distance analyses were performed based on 18S rDNA, 5.8S rDNA, ITS2 rDNA, 5.8S-ITS2 rDNA, as well as the combined 18S-5.8S-ITS2 rDNA sequence. The results indicated that C. ellipticum in Chongqing exhibits significant intraspecific genetic variation, and haplotype distribution from the five districts exhibited no significant correlation with geographical origins, presumably owing to cross-regional circulation and mixed farming practices of grass carp fingerlings. Among all molecular markers used, the concatenated 18S-5.8S-ITS2 rDNA sequence showed the highest resolution, detecting 10 variable sites and defined 16haplotypes (H_d =0.8929), with intraspecific genetic distances ranging from 0.001 to 0.003. Furthermore, the ITS2 rDNA sequence of C. ellipticum was reported for the first time in the present study, and four fixed nucleotide substitutions were detected in the 18S rDNA sequences between Chongqing and Hubei population, indicating potential deep genetic divergence between them. This study provides new molecular markers and fundamental data for the accurate identification and future population genetic studies of C. ellipticum.