Protein and isozyme markers were used to characterize 20 elite cultivars of ginger. Four different isozymes (acid phosphatase, esterase, peroxidase and polyphenolic oxidase) were analyzed to assess the genomic relationship among 20 varieties of ginger. Buffer soluble protein was isolated and resolved in SDS-PAGE. A total of 108 types of proteins were resolved, out of which 33 were unique. A total of 85 bands were detected for 4 isozymes, among them only 3 were found to be unique. The dendrogram constructed based on pooled data (protein and isozyme) divided the varieties into two major clusters each containing 10 members, respectively. The varieties Singjhara and Waynad local were found to be the most closely related while Singjhara and Sleeva local were distantly apart. The present study gave an indication of usefulness of the isozyme and protein markers for genetic discrimination between different varieties of ginger. The result of the present investigation will help in future breeding program.