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Brinjal (Solanummelongena) belonging to the family solanace brinjal fruit are a good source of calcium,phosphorus,iron and vitamins particularly B group. In addition Brinjal have much medicinal value .In can block free radicals, helps to control cholesterol level. The geniviness of a hybrid purity is one of the most important characteristics of good quality seeds. The confirmation of genetic purity in seeds is very important for identification of genetic and as well as at a commercial level.The recent advances in molecular marker proves its efficiency in the genetic purity analysis than conventional method (GOT).The main objective of this study to identify the genetic purity of the brinjal hybrids and its parental line with the help of molecular markers. In the present research 18 ISSR and 10RAPD primers were selected for the study of 3 EGG PLANT hybrids (AS 1001, AS1002, AS1003)and its parental line. All primers shows good amplification but only one ISSR & one RAPD primers produced unique fingerprint across the hybrids. ISSR primer UBC 807 for (ASH1002,ASH1002)likewise RAPD primers B18 for ASH1003 thus our study showed that aid of molecular marker are more reliable, highly efficient and reproductive for assessing fingerprinting of brinjal commercial hybrid seed`s with more accuracy.