Two-thirds of the world's overall production of protein feed ingredients, along with all other main oils and fish meals, are produced from soybeans. Genetic variability and relationships among genotypes can be examined using SDS-PAGE of seed storage proteins. In this study, seven Egyptian soybean varieties were assessed for variation in whole seed proteins using SDS-PAGE, which showed an overall of 11 protein bands with diverse molecular weights. To distinguish these soybean genotypes, precise bands of their seed storage protein profiles can be used as markers. In addition, using of five ISSR primers for genome fingerprinting produced a total of 23 ISSR bands which ranged between 990 bp and 248 bp. Of which ten ISSR bands were polymorphic, 6 bands were monomorphic, and 7 bands were unique. SDS-PAGE profiles and ISSR markers revealed the genetic relatedness among the seven soybean genotypes. Cluster analysis based on ISSR data separated the soybean varieties into several sub-clusters, which indicated that ISSRs are more differentiating than did SDS-PAGE. These results could greatly assist in the identification, breeding and preservation of the soybean germplasm.