DNA barcodes using certain regions of the genomic DNA have become a popular diagnostic tool to assign speciesspecific signatures. In plants, a number of chloroplast DNA regions such as psbA-trnH of size 400 bp have been shown to successfully discriminate members of various taxa. However, the technique is not always successful, as in the case of museum specimens or samples used in raw drug trade, where the DNA is often degraded. In this context, recent studies have suggested the use of shorter stretches of the region, called mini-barcodes, to resolve species identity. The minibarcodes are relativelymore stable and easily recovered from the degraded DNA. In this study, an attempt has been made to compare the effectiveness of mini-barcodes over full-length DNA barcodes in differentiating 16 species of Phyllanthus (Phyllanthaceae) used in the raw drug trade. Using an in silico approach, mini-barcodes of varying lengths (50–200 bp) of the region psbA-trnH were generated and evaluated for their ability to resolve the 16 Phyllanthus species in comparison to the full-length DNA barcode of size 398 bp. Results have been discussed in the light of the overall utility of mini-barcodes in resolving the species identities. First developed in animal systems, barcodes were used to demonstrate the ability of the mitochondrial gene cytochrome c oxidase subunit I (COI, 650 bp) to completely resolve over 200 closely related species of Lepidopterans (Herbert et al. 2003). Since then, the COI has been effectively used as ‘universal DNA barcode’ in several animal groups such as birds, butterflies, amphibians and fishes (Hebert et al. 2003; Gu et al. 2011). However, in plants, the COI was found to be ineffective in discriminating the taxa, because the region has a very low divergence rate (Cho et al. 2004) and is prone to rapid change in genome structure (Adams and Palmer 2003). Against this failure, the Consortium of Barcode of Life (CBOL) programme evaluated seven other potential DNA barcodes using 907 plants representing 445 angiosperms, 38 gymnosperms and 67 cryptogamic species. The seven potential regions, all from the chloroplast, were atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer and trnH-psbA (CBOL 2009). Among these, CBOL recommended the combination of rbcL and matK as the potential plant DNA barcode (CBOL 2009). However,besides these, several regions such as trnH-psbA were also found to be very effective (Kress and Erickson 2007). The latter region is easy to amplify and is one of the most variable intergenic spacers in plants (Shaw et al. 2007). This region has been successfully used in many studies (Gonzalez et al. 2009; Kress et al. 2009, 2010) and can be used as a supplementary barcode for plants. In a previous study, we showed that the psbA-trnH region could effectively resolve 16 species of Phyllanthus that were used in raw herbal trade in India (Srirama et al. 2010). Thus, using DNA barcodes or DNA signatures, it is possible to effectively discriminate species used in herbal trade and further identify adulterating plant material, if any, in shipments of raw herbal trade material. However, the success of the technique as an identification service depends upon the ease of DNA extraction and its subsequent amplification at the desired gene region. Since, the raw herbal drug material are very dry and not stored under ideal conditions, the DNA is either sheared or not very appropriate for amplification. Failure in amplifying and sequencing the degraded DNA of museum samples has been reported earlier (Whitfield 1999; Hajibabaei et al. 2005, 2006; Meusnier et al. 2008). In an attempt to address this constraint and still be able to resolve species with degraded DNA in museum samples, in processed food products and in raw drug trade, several studies have explored the possibility of using short stretches of DNA as ‘mini-barcodes’ (100–300 bp) to distinguish the species. In contrast to the regular bar codes that range between 300 bp–1 kb, the mini-barcodes are usually stable and easily recovered from degraded DNA (Hajibabaei et al. 2006; Meusnier et al. 2008; Zimmermann et al. 2008). Utility of mini-barcodes have been successfully demonstrated in a number of plants (Sonstebo et al. 2010), fishes (Hajibabaei et al. 2006; Meusnier et al. 2008; Saitoh et al. 2008; Baumstegier and Kerby 2009; Ficetola et al. 2010; Hajibabaei andMcKenna 2012), reptiles (Dubey et al. 2010), birds (Lee and Prysjones 2008; Meusnier et al. 2008; Patel et al. 2009), arthropods (Dean and Ballard 2001; Hajibabaei et al. 2006; Meusnier et al. 2008; Houdt et al. 2009; Smith and Fisher 2009; Rougerie et al. 2010; Hajibabaei et al. 2011), fungi (Meusnier et al. 2008; Houdt et al. 2009), mammals (Meusnier et al. 2008; Ficetola et al. 2010) and insects (Meusnier et al. 2008). In this study, we compared the effectiveness of minibarcodes over full-length DNA barcodes in discriminating different species of Phyllanthus (Phyllanthaceae) used in raw drug trade. Themini-barcodes of varying lengths (50–200 bp) of the region psbA-trnH were generated and evaluated using an in silico approach for their ability to resolve the 16 Phyllanthus species. The results are discussed considering the overall utility ofmini-barcodes in resolving species identities.