In the present scenario herbal medicines gaining popularity due to their effectiveness and less side effects. It is necessary to control the quality of such drugs to ensure safety of the patients. In the herbal medicine world marker compounds are used to control their quality. In the present study embelin plant marker was isolated from Embelia ribes plant using soxhlet and percolation methods. The isolated embelin was analyzed using UV, HPLC and HPTLC methods. Both the isolation methods were statistically compared for their superiority in terms of %yield and purity. Also the developed and validated methods were applied to the marketed formulation containing embelin. The studies showed that the quality and purity of reference standard compound depends on the method of isolation and the quality of the herbal raw material and its finished product depends on the nature of preparation and process of extraction.