For comparative zoology, proper recognition of basal taxa is indispensable, and in this the choice of a suitable gene with high phylogenetic resolution is crucial. For the goals of species identification in animals, the cox1 has been introduced as standard marker. Making use of the difference in intra- and interspecific genetic variation–the DNA barcoding gap- has been successful in species identification across a wide array of taxa but in some cases failed to delimit the species boundaries of closely allied allopatric taxa or of hybridising sister taxa. Here, we extend the sample size of prior studies in birds for cox1 (756 species) and target especially species that are known to be closely related and/or are known to hybridise. We compare the effectiveness of cox1 barcodes for the identification of bird species on a global scale. To obtain a larger data set, we include also DNA sequences of two other mitochondrial genes cytochrome b (2087 species) and 16S (498 species), which allows inclusion of many additional taxa. The three genes taken together, the analysed sequences comprise 2719 species of birds. Our results showed that a wide gap exists between intra- and interspecies divergences for both cox1 and cob whereas no such gap is seen for 16S. Most of the closely related species that are known to hybridise, however, showed average divergences that were intermediate between intraspecific and interspecific distances for both cox1 and cob. This study confirms, DNA barcoding in closely related and potentially hybridising species should not rely on mtDNA alone

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