Background The genetic improvement in growth and food habit domestication of largemouth bass ( Micropterus salmoides ) have made breakthroughs in past decades, while the relevant work on disease resistance were rarely carried out. Major histocompatibility complex ( MHC ) genes, which are well known as their numbers and high polymorphisms, have been used as candidate genes to mine disease-resistant-related molecular markers in many species. Methods and results In present study, we developed and characterized 40 polymorphic and biallelic InDel markers from the major histocompatibility complex genes of largemouth bass. The minor allele frequency, observed heterozygosity, expected heterozygosity and polymorphic information content of these markers ranged from 0.0556 to 0.5000, 0.1111 to 0.6389, 0.1064 to 0.5070, and 0.0994 to 0.3750, respectively. Three loci deviated significantly from Hardy-Weinberg equilibrium, while linkage disequilibrium existed at none of these loci. Conclusion These InDel markers might provide references for the further correlation analysis and molecular assisted selection of disease resistance in largemouth bass.