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Fusarium oxysporum Schlecht. f.sp. melongenae (FOM), Verticillium dahliae (Ve) and Ralstonia solanacearum are major limiting pathogens affecting eggplant cultivation and their yield in the world. Natural resistance genes are the most environmentally friendly method to control the disease. Thus, marker-assisted selection (MAS) is preferred as a tool for screening resistance genes (R-genes) in eggplant resistance breeding. In this study, markers that are specifically linked to major disease resistance genes conferring resistance to F. melongenae, V. dahliae and R. solanacearum were tested in a population containing breeding materials to validate the resistance. Resistant Solanum melongena accessions LS1934 and LS2436 and their reciprocal crosses were used as the resistance resource for this validation study. Moreover, classical resistance tests to FOM and Ve were performed with the root-dip inoculation method for classification of all the accessions based on their resistance/susceptibility responses. The SCAR426, CAPs_903 and SIVR844 markers were highly informative for the determination of resistance genes (Fomg, Ve and ERs1). Therefore, in areas with high susceptibility to diseases, a highly efficient combination of the relevant R-genes and their pyramiding into commercial eggplant varieties are proposed to be implemented as a pragmatic approach.