Quaternary vertebrate extinctions attract wide interest because of the role ascribed to humans as agents of extinction, through either over-hunting or altering habitat. This paper examines faunal and floral records from the archaeological site at Tunnel Cave, Leeuwin–Naturaliste Region, southwestern Australia, which are relevant to the Mid-Holocene local extinction of Black-flanked Rock-wallaby (Petrogale lateralis). Possible factors causing the population decline include inter-species competition, over-hunting by humans or other predators, or vegetation habitat change caused by climate change or changes in human firing practices. Identification of macroscopic charcoal excavated at Tunnel Cave shows that changes in canopy trees began from 10,000 BP, consistent with post-glacial rainfall increases, and probably causing the encroachment of closed habitats and loss of grazing areas. These changes are consistent with other faunal shifts at Tunnel Cave and with faunal and identified charcoal records from the nearby Devil's Lair deposit. There is little evidence for changes in competitor or predator behaviour, although increasing geographic isolation of Petrogale habitats possibly exacerbated predator impacts. The timing of human occupations at Tunnel Cave in relation to vegetation change suggests that human firing was a minor influence on forest composition or structure. Petrogale's Mid-Holocene disappearance from the region is therefore attributable to climatically driven encroachment of closed habitat.