To evaluate the application potential of single nucleotide polymorphism(SNP) chip in the construction of the base population for breeding, three different populations (EE, PP and SS) of Litopenaeus vannamei were challenged by Vibrio parahaemolyticus (Vp_AHPND), and the genomic information of 146 samples was obtained using the independently developed 40K SNP liquid chip “Yellow Sea Chip No.1”. The genetic background was systematically investigated and acute hepatopancreatic necrosis disease (AHPND) resistance of populations was estimated. The Vp_AHPND challenge test indicated that there were differences in disease resistance between different populations. When the overall mortality was more than 50%, the survival rate of PP population was 12.9% and 11.6% higher than that of EE and SS populations, respectively. The phylogenetic tree was constructed by using 38148 SNP markers after quality control. The result showed that the individuals of the same family first clustered together, and then the multiple families of the same population clustered together. Principal component analysis and genetic structure analysis also implied that the 146 individuals could be accurately divided into 3 groups, which was consistent with the phylogenetic tree. The analysis of genetic diversity for three populations showed that the average value of observed heterozygosity (H_o) was 0.25-0.29. The average value of polymorphic information content (PIC) was 0.20-0.23. The differences on the above three parameters between three populations were very significant (P < 0.01). The coefficient of genetic differentiation (F_ST) among the three populations was 0.11-0.21, indicating that there was medium-high level of genetic differentiation. Genomic inbreeding analysis showed that the average inbreeding coefficients of EE, PP and SS populations were −0.05±0.06, 0.20±0.09 and 0.37±0.07, respectively. Some individuals of PP and EE populations showed high levels of inbreeding. Using single step genomic BLUP with metafounder(sssGBLUP-MF) model with genotype, phenotype and pedigree information, the estimated heritability of survival after Vp_AHPND infection was medium (0.24±0.07), indicating that the base population had a promising breeding potential. To summarize, the efficiency of constructing and evaluating the base population can be further enhanced by using the liquid chip "Yellow Sea Chip No.1".