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Capsicum annum [L.] is one of the most economically important vegetable crops in India. In order to assess the genetic relation,DNA from thirteen capsicum cultivars were screened using inter simple sequence repeat (ISSR) and microsatellite (SSR)markers. Five ISSR primers amplified 204 reproducible bands of which 139 were polymorphic. The percentage of polymorphicbands detected by ISSR was 100%. The highest polymorphic bands obtained by the use of primers UBC-809 (34) and UBC-66(53). A total of 1-5 alleles were detected by six SSR primers, with an average of two alleles per primer. The number of alleles perlocus ranged one (ssrCAMS-811) to five (ssrCAMS-142). The polymorphism information content (PIC) values ranged from 0.27(ssrCAMS-405) to 0.67 (ssrCAMS - 142). This study reveals the great importance of guaranteeing the differentiation of chillicultivars and the application for certification purposes