Phylogenetic relationship among local and exotic genotypes of Capsicum were elaborated through morphological characterization and molecular markers.Protocols for isolation of total genomic DNA and seed storage proteins were optimized for Capsicum genotypes. Four RAPD primers were used to amplify genomic DNA. Unweighted Pair Group of Arithmetic Means (UPGMA) estimates of Genetic distances (GD) using RAPD primers ranged from 0 to 100%. Total seed storage proteins profile of the genotypes using SDS-PAGE analysis showed high range of genetic distances i.e. from 0-100% among various comparisons.The data obtained from PCR and SDS-PAGE was also used to study phylogenetic relationship through constructing two independent dendrograms. Dendrogram based on DNA data showed that the twenty-five genotypes were clustered into four groups.No such grouping was visible in the dendrogram based on the SDS-PAGE. Hence it was concluded that DNA based data is more useful for phylogenetic elaboration of Capsicum genotypes. Further morphogenetic and taxonomic study is recommended for assessment of the exact taxonomic status of genotypes segregated into different groups.