Holocene vegetation records are presented from palaeochannels in the southern Kelabit Highlands, at Pa’Dalih (PDH 212) and at Pa’Buda (BPG), and from a peat bog in the northern Kelabit Highlands, at Bario (Ba). Results are based on changes in the sediment lithology, loss-on-ignition, magnetic susceptibility, pollen, phytoliths and other palynomorphs. At Pa’Buda, possible clearance occurred ~6500 cal. BP, perhaps for arboriculture. More pronounced signatures of clearance are at PDH 212 by ~3100 cal. BP, and at Ba by 1300 cal. BP. Propagation/cultivation of the sago palm, Eugeissona , may have been taking place by ~2800 cal. BP at site PDH 212 and was probably taking place by at least 1300 cal. BP at Ba. Rice cultivation may have been taking place between 2800 and 1200 cal. BP at PDH 212, but this remains speculative, due to the morphological features of the Oryza bulliforms, but it was likely taking place at Pa’Dalih by 530–490 cal. BP, where Oryza bulliforms, with characteristics similar to domesticated types are present, and there was a sharp rise in sedimentation, caused by intense burning. At Ba, within the last 600 years, an increase in Palmae phytoliths may signify increasingly intense human impact. In more recent times, both rice and banana cultivation are represented in the phytolith record at Pa’Buda.