For over a decade, molecular short standardised DNA fragments, termed DNA barcodes, have been developed for species discrimination around the world. As of 2010, the vast majority of barcoding research was biased toward particular taxonomic groups and geographic regions largely because researchers in developed countries were the ones with the resources and capacity to carry out such work. To rectify this, the International Barcode of Life Project was launched with the intent to extend the geographic and taxonomic coverage of the barcode reference library. South Africa committed to this mission in an attempt to catalogue all of its known biodiversity and, possibly, help identify new species. To date, approximately 48 000 South African faunal barcodes are housed in the Barcode of Life Data System (BOLD), which represent only 2.3% of all known South African animal species. Although insects are the best represented in absolute terms, with over 37 000 samples recorded, they are still grossly lacking with just over 1% representation. Much like the global trend, there is a general taxonomic bias, with fish, birds and mammals showing the greatest representation. Moreover, geographic bias is also present, with the Free State province particularly under-represented on BOLD, likely owing to limited human capacity. Although few studies have been published with respect to barcoding, the majority reveal that the cytochrome c oxidase 1 (CO1) gene, used in isolation or in conjunction with other molecular markers, can greatly benefit South African biodiversity research. Several limitations of DNA barcoding are discussed and recommendations specific to South Africa provided.