According to International Barcode of Life Project (http://ibol.org/about-us/what-is-dna-barcoding/), DNA barcoding first came to the attention of the scientific community in 2003 when Paul Hebert’s research group at the University of Guelph published a paper titled "Biological identifications through DNA barcodes". In it, they proposed a new system of species identification and discovery using a short section of DNA from a standardized region of the genome. That DNA sequence can be used to identify different species, in the same way a supermarket scanner uses the familiar black stripes of the UPC (Universal Product Code) barcode to identify your purchases.
The gene region that is being used for almost all animal groups, a 648 base-pair region in the mitochondrial cytochrome c oxidase 1 gene (“CO1”), is proving highly effective in identifying birds, butterflies, fish, flies and many other animal groups. The advantage of using COI is that it is short enough to be sequenced quickly and cheaply yet long enough to identify variations among species.
The COI barcode is not effective for identifying plants because it evolves too slowly, but two gene regions in the chloroplast, matK and rbcL, have been approved as the barcode regions for land plants.