The late Quaternary fossil vertebrate faunas from caves and cliff sites in the limestone of Mt Cookson, near Waiau in North Canterbury, are described. These faunas allow documentation of faunal changes in the area, over the last 40,000 years, and reveal differences from other previously studied areas that are related to climate. Pitfall faunas from the numerous potholes dominate the deposits, but three predator‐accumulated deposits, attributed to the New Zealand falcon Falco novaeseelandiae, were found. The deposits in Merino Cave and Holocene Hole were studied in detail.Merino Cave had two distinct fossil faunas, from which six radiocarbon dates were obtained, showing that deposition spanned the Otiran Glacial period, between 38,000 yrs BP and 14,000 yrs BP. The older of the two Merino Cave faunas, dated at about 38,000 yrs BP, is the first extensive assemblage for the mid‐Otiran period from New Zealand. The moa fauna was dominated by the heavy‐footed moa Pachyornis elephantopus, but the stout‐legged moa Euryapteryx geranoides, upland moa Megalapteryx didinus, large bush moa Dinornis novaezealandiae, and slender moa D. struthoides were present. Carinates included the following: Eyles's harrier Circus eylesi, adzebill Aptornis defossor, large kiwis Apteryx australis or A. haastii, weka Gallirallus australis, New Zealand quail Coturnix novaezelandiae, Finsch's duck Euryanas finschi, kea Nestor notabilis, laughing owl Sceloglaux albifacies, and owlet‐nightjar Aegotheles novaezealandiae. This assemblage indicates an open shrubland ‐grassland environment. The younger Merino Cave fauna was deposited between 20,000 and 14,000 years ago, during the last major glacial advance at the coldest time of the Otira Glaciation. Only moa bones were present, and P. elephantopus again dominated the fauna. This late Otiran population comprised larger individuals than did the mid‐Otiran population, indicating mean size of individuals got bigger as the climate cooled.Holocene Hole had a rich deposit of small birds dating from the late Holocene, between 3,000 and 2,400 yrs BP. This fauna was deposited when continuous beech forest clothed the landscape. By then the large emeids P. elephantopus, E. geranoides, and M. didinus had been replaced in the fauna by the little bush moa Anomalopteryx didiformis in association with the large bush moa D. novaezealandiae. New Zealand quail and pipits Anthus novaeseelandiae were absent from the local fauna which was dominated by a range of forest species. However, the presence ofadzebills and Finsch's ducks, both absent in Holocene forests farther west, reflects the low rainfall and seasonal dryness of the area. Several species of petrels were present on Mt Cookson: Mottled petrels Pterodroma inexpectata. Cook's petrel Pterodroma cookii, shearwaters Puffinus sp., and diving petrels Pelecanoides urinatrix.The falcon deposits were dominated by bones of kiore Rattus exulans, and included a few bones of species introduced to New Zealand by Europeans, indicating that most of the remains were deposited in the last 800 years, or during the post‐human contact period. However, bones of a wide range of bird species, numerically dominated by parakeets Cyanoramphus sp., were also present. Quail and pipit were common, and ternbirds Bowdhria punctala were present, indicating the re‐establishment of shrublands or grasslands in the area during the post-human period. A small amount of material was older, as indicated by preservation characteristics and a single date of about 2,000 yrs BP. This older material contained the following species not present in material of postrat age: wrens Xenicus sp., snipe Coenocorypha cf. aucklandica, short-tailed bats Mystacina sp., Duvaucel's gecko Hoplodactylus duvaucelii, and tuatara Sphenodon sp. These taxa are now extinct or confined to rat-free islands, so these fossil records support the contention that kiore were responsible for the reduction in their mainland ranges.