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This research employs a modern analogue approach to examine relationships between pollen, vegetation change, and land use in the tropical environments of Island Southeast Asia over the past ~5000 years. Interpretation of fossil pollen data relies upon uniformitarian principles. Few modern pollen- vegetation studies from the region exist, and those that do have focused on climatic or ecological aims. Main contributions of this study are: the collection and analysis of modern botanical data and pollen assemblages from various human-modified and ‘natural’ vegetation types; and the comparison of this modern dataset with fossil pollen sequences in order to test hypotheses relating to signatures of past land use. Some fossil assemblages showed statistical similarity with those from modern ‘cultured’ landscapes, whilst others aligned more closely with those from natural vegetation. Cores from the northern Kelabit Highlands of Sarawak, Malaysian Borneo, contain assemblages from 1700 cal BP onwards that are similar to those produced by modern arboriculture; a core from the southern Highlands contains fossil assemblages as old as 2000 cal BP that align with those from modern wet rice paddies. These ages coincide with the earliest archaeological dates from nearby sites. Earlier vegetation changes appear to relate to edaphic development and climatic fluctuations. In northern Palawan, western Philippines, the first fossil pollen sequence from the island records post-5000 cal BP marine regression, hydrological fluctuations that are likely related to ENSO cyclicities, and persistence of open landscapes with minor evidence of closed forest after 2750 cal BP. This contrasts with existing proxy data that imply increasingly closed forest through the Holocene. In a region where direct archaeobotanical evidence is sparse, and little modern pollen- vegetation work has been done, this research contributes to clarifying modes and timings of changes in subsistence-related disturbance, as well as bolstering recent interpretations from other palaeoclimatic proxies for ENSO intensification from ~4000 cal BP. These results, and those from similar future studies, can provide baseline data for long-term monitoring and conservation initiatives.