Field and Laboratory experiments were carried out at Gemmiza Experimental Research Station during 2002 and 2003 growing seasons, with the objectives of identifying morphological and biochemical characteristics of commercially released soybean varieties namely Giza/21, Giza /35, Giza /111, Crawford, and some promising genotypes viz., Hybrid1/10, Hybrid 1/12, Hybrid /85, Hybrid 88/1, Hybrid 8W3 , Hybrid 93, Giza /30, Giza/32. Twelve soybean (Clycine max L Merr) genotypes were identified based on morphological differences in seed, seedling and adult plant; agronomic characters such as days from planting to flowering and maturity, yield and its components, in addition to seed chemical composition and biochemical variability of genomic fingerprinting. Field observations indicated that some genotypes were indistinguishable from each other by using phenotypic and agronomic characteristics. Furthermore, genotypic differences in agronomic and chemical characteristics (protein, Carbohydrate and fats) can be affected by environmental conditions prevailing in the field. DNA analysis was considered essential to distinguish among genotypes where protein banding patterns were effective in providing resolution for soybean genotypes. The results of this study will increasingly become important in variety registration and breeders rights .