We report the characterisation of mitochondrial and nuclear gene sequences from bone tissue of a New Zealand‐endemic extinct avian vertebrate. We present evidence that we have successfully obtained huia‐specific DNA sequences from the mitochondrial 12S rRNA gene and the nuclear cMos proto‐oncogene. These gene sequences have allowed us to carry out the first phylogenetic studies of this extinct species which confirm that the huia is a member of the Passeriformes lineage of birds.