The invention discloses a molecular genetic breeding method for California weever. The method comprises the steps of selecting basis parent fishes, establishing families, carrying out group breeding selection based on production cells, selecting and breeding parent fishes in the second generation families for hybridization, and repeating the above steps to obtain the third generation fishes. (1) The breeding method can efficiently breed a group with better characters, clear genetic backgrounds, larger gene pool and stable inheritance; (2) the breeding method can quickly screen parents with better characters to solve the problem of inbreeding depression; (3) the breeding method can directly breed fishes and select breeding in a large water body and directly carry out breeding selection under the environmental condition of production breeding, in this way, the result of breeding selection is more representative, the influence of environmental genes on fish growth can be further exerted so that genes of the breeding selection can make complete expression, in addition, the purpose that scientific research is combined with production is achieved, and when the breeding selection is carried out, production can be optimized, thereby acquiring a win-win effect.