Abstract: The hybrid triploids of Megalobrama amblycephala (♀) × Culter alburnus (♂) were successfully induced by using hydrostatic pressure technique, achieving a high triple ploidy rate (98.5%), high survival rate (80.06%), and fast growth. In this study, the morphological distribution and genetic structure of the intermuscular bones in hybrid triploid of M. amblycephala × C. alburnus were further studied. The results showed that the average number of intermuscular bones in the hybrid triploid (MC-3n), hybrid diploid (MC-2n), M. amblycephala (MA), and C. alburnus (CA) were 129.4, 129.0, 124.5, and 137.6, respectively. There was no significant difference in the number of intramuscular bones between MC-3n and MC-2n (P>0.05), but there was a significant difference between the hybrids and their parents (P<0.05). All four populations exhibited 7 types of intermuscular bones with no significant difference between the left and right sides. The average alleles of the four populations were 4.55, 4.15, 4.05, and 3.30, respectively. The average observed heterozygosity was 0.8817, 0.7967, 0.8250, and 0.5550, while the average expected heterozygosity was 0.6740, 0.6435, 0.6325, and 0.4941, respectively. The average polymorphic information content was 0.6081, 0.5780, 0.5632, and 0.4298, respectively, indicating rich genetic diversity in both MC-3n and MC-2n, with slightly higher diversity in MC-3n. Hardy-Weinberg equilibrium analysis showed that all four populations exhibited heterozygote excess at most loci (D>0) and heterozygote loss at only a few loci (D<0). The genetic similarity showed that MC-3n and MC-2n were more similar to their maternal parent than to their paternal parent, with a lower genetic distance to the mother, indicating a certain maternal effect. The clustering analysis demonstrated that MC-3n clustered first with MC-2n, then with MA, and finally with CA, consistent with the genetic distance. This study provides reference for the breeding and subsequent application of hybrid triploid of M. amblycephala × C. alburnus.