We have done comparative morphological and chemotaxonomic studies to investigate the phylogenetic relationship of different accessions within the Podophyllum species. HPLC profiles revealed that all Podophyllum hexandrum accessions collected from different geographical locations are chemically highly diverse. Also, we have observed that chemotaxonomic studies clearly demonstrated that chemical characters of the Podophyllum hexandrum are suitable to generate essentially the same relationship as revealed by RAPD analysis.