In this study, 151327 of InDels were in silico identified by taking advantage of whole genome re-sequencing of two eggplant (Solanum melongena) lines. The primers targeting 180 InDel loci were developed, which were subjected in tests of two re-sequencing eggplant lines and derived hybrid line. Out of that, sixty-two (34.7%) of total primers were polymorphic between both varieties. In addition, the genetic diversity and specificity of 24 eggplant lines and 143 varieties were investigated by use of these markers. The results from purity test of variety from two InDel markers matched well with those from field experiments.