The invention discloses a molecular breeding method of new varieties of cynoglossus semilaevis and solves the problems that in current cynoglossus semilaevis breeding and cultivation, an intraspecific hybridization method has high randomness and low good variety breeding probability and a group breeding method causes inbreeding easily and thus causes reduction of economic traits and productivity. The method comprises breeding steps as follows: 1, selecting phenotypic characters; 2, detecting and analyzing genetic composition of male and female parents; 3, selecting parents in different breeding family trees, and performing grouping with the genetic distance between the parents of 0.7-1.0 as the threshold range; 4, breeding offspring until sexual maturity; 5, with cynoglossus semilaevis offspring as a new generation of parents, repeating operation in steps 1 to 4 until meeting the design requirement of the new varieties of cynoglossus semilaevis. According to the method, during breeding of the new varieties of cynoglossus semilaevis, the breeding family tree of each generation of parents is detected all the time, grouping is performed with the genetic distance between the parents of 0.7-1.0 as the threshold range, inbreeding can be avoided, the characters of the new varieties of cynoglossus semilaevis can be selected in the set direction, the economic characters and productivity can be significantly improved, and the probability of occurrence of superior new varieties can be increased.