According to Hebert et al. (2003) animal species can be distinguished by comparing a 648-bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. The COI barcoding can be used for two purposes:

• detection of new species
  
• identification of known species

In both cases, query sequences are compared with COI sequences stored in reference libraries like GenBank and BOLD (Barcode of Life Data Systems). 

References/Literature

Čandek K, and Kuntner M (2014), DNA barcoding gap: reliable species identification over morphological and geographical scales, Mol. Ecol. 15, 268-277. (abstract)

Hebert PDN, Cywinska A, Ball SL, and deWaard JR (2003), Biological identifications through DNA barcodes, Proc. Roy. Soc. Lond. B 270, 313-321. (pdf) 

Kekkonen M, and Hebert PDN (2014), DNA barcode-based delineation of putative species: efficient start for taxonomic workflows, Mol. Ecol. Resour. 14, 706-715. (pdf)

Lijtmaer DA, Kerr KCR, Stoeckle MY, and Tubaro PL (2012), DNA barcoding birds: from field collection to data analysis, in: “DNA Barcodes’” (Kress W, and Erickson D, eds.), Methods in Molecular Biology, vol. 858. (link) 

Meiklejohn KA, Damaso N, and Robertson JM (2019), Assessment of BOLD and GenBank – their accuracy and reliability for the identification of biological materials, PLoS ONE 14, e:0217084. (pdf)

Paulay G, and Meyer CP (2005), DNA barcoding: error rates based on comprehensive sampling, PLOS Biol. 3, e:422. (pdf)

Ratnasingham S, and Hebert PDN (2007), BOLD: the barcode of life data system (www.barcodinglife.org), Mol. Ecol. Notes 7, 355-364. (pdf)

Savolainen V, Cowan RS, Vogler AP, Roderick GK, and Lane R (2005), Towards writing the encyclopaedia of life: an introduction to DNA barcoding, Philos. Trans. R. Soc. Lond. B 360, 1805-11. (abstract)

Shen YY, Chen X, and Murphy RW (2013), Assessing DNA barcoding as a tool for species identification and data quality control, PLOS ONE 8, e:57125. (pdf)