Two varieties (indigenous and hybrid) of pumpkin (Cucurbita maxima) are cultivated and widely used as food sources in Bangladesh. The aim of this study is to compare nutrient contents in different parts of two varieties of pumpkin. The nutritional compositions were analyzed by standard methods. Fatty acids and amino acids were analyzed by GC/MS and amino acid analyzer. The proximate compositions analysis data indicate that a higher amount of moisture (p < 0.001) and fat (p < 0.01) were observed in the seed of indigenous but the seed of hybrid were rich in crude fiber (p < 0.01) and carbohydrate (p < 0.001). On the contrary carbohydrate content was predominant in the flesh (p < 0.05) and peel (p < 0.01) of indigenous. The energy content was high in the peel, seed and flesh of indigenous (p < 0.001, 0.001 and 0.05 respectively). A significant amount of reducing sugar was found in the peel, flesh (p < 0.05) and seed (p < 0.001) of hybrid. Vitamin C content was high in peel (p < 0.001) and seed (p < 0.01) of indigenous and only in the flesh (p < 0.001) of the hybrid. A remarkable amount of Na, K, Fe and Zn were present in peel (p < 0.001) of hybrid. The notable amount of P and Cu (p < 0.01) were present in the seed and K, Fe and Ca (p < 0.001) were in the flesh of indigenous. The seed of hybrid was enriched with saturated fatty acid (capric acid, p < 0.001; myristic acid, p < 0.01 and stearic acid, p < 0.05), whereas unsaturated fatty acids (oleic, linoleic and linolenic acid, p < 0.05) were rich in the seed of indigenous. A significant amount of threonine, serine, methionine, isoleucine and tyrosine were present in the seed of indigenous (p < 0.01) but only alanine in the seed of hybrid (p < 0.01). These results suggested that a considerable amount of nutrients were present in all three parts of the two varieties, thus both varieties could be the potential source of nutraceuticals.