Background: Makhana is generally used as a health promoting diet especially for weight loss and anti-aging effect. Identification and quantification of different biomolecules and their related acrivities in human cells are important. Methods: In this study, two varieties of makhana viz; Superior Selection-1 (SS-1) and Swarna Vaidehi have been selected for proximate compositions and nutrient components especially for anti-obesity bio-molecules by using standard methods. Result: The biochemical constituents of the SS-1 revealed moisture 12.38%, protein 11.02%, carbohydrates 73.50% and fat 0.45%. The minerals content of SS-1 were Ca2+ 149.18±1.68 mg/100 g, Mg2+ 20.0±0.81 mg/100g and S2+ 60.6±1.70 mg/100 g, which were higher than that of Swarna Vaidehi. The Swarna Vaidehi variety contained moisture 14.75%, protein 8.0%, carbohydrates 77.33% and fat 0.35%. The resistant starch, amylose of makhana ranged from 17.0±0.83 (SS-1) to 18.6±0.57% (Swarna Vaidehi). The free amino acids like glutamic acid, tyrosine, alanine, lysine, leucine were commonly found in both the varieties. In addition, the amino acids arginine and histidine content in SS-1 were 12.10±0.24 g/100 g p and 2.70±0.25 g/100 g p, respectively, whereas Swarna Vaidehi possessed 10.70±0.33 g/100 g p and 3.10±0.18 g/100 p, respectively. The amino acids tyrosine and phenylalanine of SS-1 were 2.70±0.41 g/100 g p and 5.88±0.49 g/100 g p as compared to Swarna Vaidehi (0.44±0.09 g/100 g p and 80±0.25 g/100 g p).