The invention belongs to the technical field of 
germplasm innovation of aquatic animals and particularly relates to a method for for breeding 
litopenaeus vannamei with WSSV (
white spot syndrome virus) resistance on the basis of multi-marker combination assistance and an application of the multi-combination markers. SNP marker 
typing is performed on SNP loci of 
immune signaling pathways of the 
litopenaeus vannamei in sensitive groups and resistance groups with a high 
throughput typing technology, and 6 SNP molecular markers in significant correlation with WSSV resistance are obtained. The optimal resistance maker combination is obtained through screening with a multi-marker interaction 
analysis method and comprises nLvALF2g-89-A>G, 
Unigene34569g-97-T>C and TRAF6g-139-A>G, and four 
genotype combinations including AA-TT-AA, AA-CT-AA, AA-CT-AG and AG-CT-AA of the three markers show an obvious correlation 
advantage with the WSSV resistance. Candidate markers are provided for 
disease-resistant 
molecular breeding of prawns, one novel path is provided for 
molecular marker assistant resistance breeding of the prawns, and broad application prospect is realized in research of WSSV-resistance variety breeding of the prawns.