DNA barcoding is a rapid method of differentiating and assigning taxonomy to species using standardized short DNA sequences. For animals, the most commonly used sequence is a 658-bp (base pair) region of the mitochondrial cytochrome c oxidase subunit I gene (COI, COX1, CO1). DNA barcoding allows for fast, reliable, automatable and cost-effective species identification by users with little or no taxonomic experience [37]. Identifications are usually made by comparing unknown sequences against known species DNA barcodes via alignment searching (BLAST) [38] or distance-based tree construction [39]. A suitable barcode for identification at the species level should be sufficiently variable between species (typically at least 3 % difference between closely related species but this may vary amongst taxonomic groups) and display either low or no intraspecific variations. Also, barcodes should be widely studied for a large number of species to enable comparison of the nucleotide sequence from an unknown sample with reference sequences in a database. Accurate species identification wholly relies on the taxonomic coverage of barcodes in a reference database. If the query sequence lacks a conspecific (belonging to the same species) target sequence in the database, species-level barcoding-based identification of the query will fail. Instead, the closest matches in the database may be identified and the sample barcode scored as a “new” taxon (operational taxonomic unit, OTU). From a practical point of view, therefore, DNA barcoding requires a comprehensive reference database. Such reference data sets are being assembled by the barcoding campaigns initiated by the International Barcode Of Life project (iBOL; www.ibol.org), resulting in considerably improved species coverage for target taxa of such DNA barcoding campaigns [40]. Official barcode sequences generated by the iBOL initiatives are deposited and organized in the Barcode Of Life Data (BOLD) Systems (http://boldsystems.org; [41]). BOLD is a large-scale and rigorously curated DNA barcode storage database, and most of the sequence information contained within BOLD has been derived from voucher specimens with authoritative taxonomic identifications. Barcoding campaigns focussing on fish, birds, mammals, insects and fungi have been initiated e.g. the Fish Barcode of Life Initiative (FISH-BOL, www.fishbol.org), the Marine Barcode Of Life Initiative (MarBOL, www.marinebarcoding.org), the Shark Barcode Of Life project (SharkBOL; www.sharkbol.org) and the Barcode of Wildlife Project (BWP; www.barcodeofwildlife.org). For plants there are initiatives to barcode e.g. the world’s tree species in TreeBOL and grasses and grass-like plants in GrassBOL. Barcodes and a variety of alternative taxonomically informative genes that have been generated from general scientific research are deposited in the International Nucleotide Sequence Database Collaboration (INSDC) and can be used for taxonomic assignment in barcoding studies. The iBOL initiative aims to create a database of 5 million standardized DNA sequences, which can be used to identify 500,000 species, by 2015. Scientific literature on the utility of DNA barcoding in the recognition, discrimination and discovery of plant and animal species has been reviewed extensively by Savolainen et al. [42], Kress and Erickson [43], Bucklin et al. [44], Hollingsworth et al. [26], Fazekas et al. [45], Ortea et al. [33], Nicolè et al. [34], Bhargava and Sharma [46], Kvist [47] and Sandionigi et al. [48].