The genus Melia L., which belongs to the 'Mahogany' family Meliaceae, is a source of important phytochemicals with marked medicinal properties. Species identification in Melia is complex due to the existence of overlapping morphological features. Though Melia dubia Cav. is listed as a synonym of Melia azedarach L., it is not clear from the available literature whether they are the same species or different, and the species complexity still remains unresolved. In the present study, ten accessions of M. dubia and M. azedarach were analysed by DNA barcoding using three chloroplast DNA markers (rbcL, matK, and trnH-psbA), and one nuclear marker (ITS2). Intra-specific divergence was not found in any of the four markers. However, the inter-specific divergence between M. azedarach and M. dubia ranged between 0.3% (rbcL) and 4.7% (ITS2) for individual markers, and for the combined dataset, it was 8.5%. Among the four markers, ITS2 was found to be the most suitable marker for