Present study was undertaken to estimate genetics diversity in local and exotic genotypes of Capsicum (chili) using SDS-PAGE analysis. Total seed proteins were extracted and separated on 12.5% Polyacrylamide gels using standard protocols. Protein fragments of various molecular weight were separated in various Capsicum genotypes. Individual protein fragments were considered as allele / loci. Estimates of Genetic Distances (GD) ranged from 0 to 100%. Nineteen Capsicum genotypes were clustered in four groups A, B, C and D comprising 7, 5 and 7 genotypes, respectively. It was concluded that genotypes Fehsil Bibber 1 and Ajay Bibber 1 were most distantly related to each other and hence it is recommended that these two genotypes should be crossed to create a segregating population with maximum genetic diversity for the improvement of chili crop in Pakistan.