Holocene New Zealand sea lion (Phocarctos hookeri) bones collected from the north of New Zealand's South Island strengthen existing evidence for the former Holocene presence of breeding colonies of P. hookeri on mainland New Zealand. The taxonomic identity of Phocarctos bones is confirmed using both morphology and ancient DNA analysis. Five radiocarbon dates on four adult and one pup bone from Creighton's Cave near Paturau, northwest Nelson, ranged from 1290±30 yr BP to 5430±30 yr BP. Three radiocarbon dates on pup bones spanning 200 14C yr (1550±30 yr BP to 1390±30 yr BP) reveal that a prehistoric breeding rookery was present at Delaware Bay, Nelson, until shortly before the time of human arrival c. AD 1280 (670 yr BP). The Delaware Bay site in particular provides a valuable snapshot of coastal New Zealand faunas shortly before human arrival, one that has potential to enhance our understanding of changes in the endemic coastal fauna associated with human colonisation.