Beak and feather disease virus (BFDV) infections are often fatal to both captive and wild parrot populations. Its recent discovery in a wild population of native red-fronted parakeets has raised concerns for the conservation of native parrots, all of which are threatened or endangered. The question of a recent introduction versus a native genotype of the virus poses different conservation-management challenges, and thus, a clear understanding of the molecular phylogeny of BDFV is a crucial step towards integrated management planning. This study represents the first comprehensive attempt to screen New Zealand's endangered and threatened psittacines systematically for BFDV. We sampled and screened kakapos (Strigops habroptilus), kakas (Nestor meridionalis), keas (N. notabilis), Chatham parakeets (Cyanoramphus forbesi), Malherbe's parakeets (Cyanoramphus malherbi), yellow-crowned parakeets (C. auriceps) and red-fronted parakeets (Cyanoramphus novaezelandiae), as well as eastern rosellas (Platycercus eximius), an introduced species that is now common throughout the North Island, for BFDV. Out of all species and populations sampled (786 individuals), we found 16 BFDV-positive red-fronted parakeets from Little Barrier Island/Hauturu, seven eastern rosellas from the Auckland region, and eight yellow-crowned parakeets from the Eglinton Valley in the South Island. The full genomes of the viral isolates from the red-fronted parakeets share 95-97 % sequence identity to those from the invasive eastern rosellas and 92.7-93.4 % to those isolates from the South Island yellow-crowned parakeets. The yellow-crowned parakeet BFDV isolates share 92-94 % sequence identity with those from eastern rosellas. The low level of diversity among all BFDV isolates from red-fronted parakeets could suggest a more recent infection among these birds compared to the yellow-crowned parakeets, whereas the diversity in the eastern rosellas indicates a much more established infection. Pro-active screening and monitoring of BFDV infection rates in aviaries as well as in wild populations are necessary to limit the risk of transmission among threatened and endangered parrot populations in New Zealand.