The invention discloses a 
genetic molecular marking combination for anti-
disease stichopus japonicas breeding and application of the 
genetic molecular marking combination and belongs to the field of 
aquatic product genetic breeding. The 
genetic molecular marking combination consists of three SNP (
Single Nucleotide Polymorphism) markers SNP88, SNP112 and SNP126 related to anti-
vibrio splendidus infection of 
stichopus japonicas, and the three marked dominant genotypes are respectively SNP88 (CC), SNP112 (AA) and SNP126 (TT). A breeding method with the genetic markers comprises the following operation steps: (1) extracting parent 
DNA (Deoxyribonucleic Acid) and 
typing; (2) selecting parents; (3) performing filial generation 
seedling breeding. By adopting the genetic molecular marking combination, effective molecular markers for improving the economic property of anti-
vibrio splendidus infection of 
stichopus japonicas are provided, the genetic markers are adopted for auxiliary 
marker selection of stichopus japonicas, anti-
disease breeding can be carried out, the anti-
vibrio splendidus infection of the stichopus japonicas can be improved, the morbidity of 
skin ulcer syndromes of the stichopus japonicas can be substantially reduced, and the combination has great significances in increasing the breeding 
survival rate and the breeding benefits.