Peel color is an important breeding objective for eggplant.Dark purple and purplish red are the most common colors in commercial eggplant cultivars.A co-dominant amplified fragment length polymorphism (AFLP) marker which was associated with the peel color (each in coupling phase to dark purple and purplish red) was found in studying the genetic diversity in 58 eggplant accessions (contained cultivars and wild relatives).The maker bands were sequenced and converted to SCAR marker,this polymorphism in sequence was from an inserted/deleted (indels) mutation.And DNA from 136 eggplant materials (inbred lines,F1,and wild relatives) were amplified with the designed SCAR primers as template,high correlation between the SCAR marker and peel color (dark purple and purplish red) was found.Then,bulked line analysis (BLA) combined with AFLP was further used to identify polymorphic fragments,and another six AFLP markers were tested and verified to be associated with peel color,which demonstrated that BLA was an useful method for identifying molecular markers of interested traits.In conclusion,these markers will facilitate the MAS (maker-assisted selection) of eggplant breeding for peel color. Peel color is an important breeding objective for eggplant. Dark purple and purplish red are the most common colors in commercial eggplant cultivars. A co-dominant amplified fragment length polymorphism (AFLP) marker which was associated with the peel color (each in coupling phase to dark purple and purplish red) was found in studying the genetic diversity in 58 eggplant accessions (contained cultivars and wild relatives). The maker bands were sequenced and converted to SCAR marker, this polymorphism in sequence was from an inserted / deleted (indels) mutation . DNA DNA from 136 eggplant materials (inbred lines, F1, and wild relatives) were amplified with the designed SCAR primers as template, high correlation between the SCAR marker and peel color (dark purple and purplish red) was found. Chen, bulked line analysis (BLA) combined with AFLP was further used to identify polymorphic fragments, and another six AFLP markers were tested and verified to be associated with peel color, which demonstrated tha t BLA was an useful method for identifying molecular markers of interested traits. In conclusion, these markers will facilitate the MAS (maker-assisted selection) of eggplant breeding for peel color.