The present study highlights the phylogenetic relationship between the Alpinia species collected from Western ghats. Maximum phylogenetic relationship is seen between A.calcarata and A.mutica. In this study we propose the trnL (UAA) intron - trnF (GAA) exon as marker for barcoding Alpinia species. Chloroplast DNA sequencing resulted in an unambiguous 396bp for Alpinia calcarata 399bp for A. malaccensis, 404bpfor A. purpurata, 383bp for A. galanga, 402bp for A. vittata, 393bp for A. mutica, 401bp for A.abundiflora.