Pungency genotyping of commercially cultivated chilli peppers of Capsicum species seggregate in to pungent and non-pungent at seed level itself using MAP1 and Csy-1 molecular markers. MAP1: A single DNA band admeasuring 494 bp was observed in 10 commercial chilli peppers, C. annuum Pragna, Teja, LCA-335, Special bullet, G-3, G-273, G-4, Badiga-1 and G-5 and C.chinense variety Kotpar. A single DNA band admeasuring 479 bp was observed in C.annuum varieties California wonder and Yolo wonder (positive control) using Pun1 allel specfic primer MAP1. Csy 1: A single DNA band admeasuring 981 bp was observed in 10 pungent chilli peppers, C. annuum Pragna, Teja, LCA-335, Special bullet, G-3, G-273, G-4, Badiga-1 and G-5 and C.chinense variety Kotpar. The DNA band corresponding to 981 bp was absent in C.annuum varieties California wonder and Yolo wonder (positive control) using capsaicin synthase gene Csy1 primer.