Chickpea (Cicer arietinum L.), a self-pollinating legume being cultivated globally as a rich source of vegetarian protein. It plays an important role in human feed and nutritional security, especially in agricultural-based communities. Chickpea has higher bioavailability of protein, good sources of polyphenols and flavonoids. Besides their nutritional value, chickpea seeds contain various phenolic compounds. Desi and Kabuli chickpeas are being used worldwide and there are few studies where both desi and kabuli chickpeas seed flour for above properties with respect to physiological traits has been reported.Fusarium wilt is one of the most destructive biotic stress reducing chickpea productivity worldwide. As a step towards understanding the basis of wilt resistance in chickpea, we investigated the morpho-physiological and biochemical traits of desi and kabuli chickpea genotypes and screened these genotypes for fusarium wilt disease using gene based molecular markers.Biochemical parameters viz., protein content, amino acid, total flavonoid content, total phenolic contents and RSA as well as two physiological traits i.e., chlorophyll content and leaf area index.