Abstract: Genetic relationship were evaluated among thirty two cultivars of Brassica rapa, collected from Bangladesh, Japan and China, by employing SDS-PAGE for seed protein and esterase, acid phosphate and peroxidase analysis. SDS-PAGE generated a total of 32 bands of which nearly 31% were polymorphic, followed by esterase of 9 bands of nearly 19% polymorphic and no identifyable polymorphic band was found from both acid phosphate and esterase analysis. However, these polymorphic markers clearly distinguished between yellow sarson and brown seeded cultivars. Cluster analysis using data generated by SDS-PAGE for seed protein, clearly separated the yellow sarson, self-compatible cultivars from the brown seeded, self-incompatible cultivars, as well as different brown seeded cultivars from Bangladesh, Japan and China origin.