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Land use change results from the interaction between the human and the natural system and therefore various scientific disciplines have developed paradigms and methods to study land use change. However, these disciplinary approaches can only cover part of the complex system of land use change. The objective of this dissertation is to develop interdisciplinary methodologies to identify and integrate factors that are important in the land use system to describe and model the land use system in a comprehensive manner. The methodological challenges that are addressed in this study include bridging differences in spatial and temporal scales and organisational levels, identification of appropriate units of analysis, combining different disciplinary paradigms and developing new paradigms that unify the disciplines in one concept. The development of these methods is illustrated with a case study in a municipality in the Philippines, where in the past century large land use changes have taken place through commercial logging and expansion of agriculture. To make projections of future land use in the area models were constructed for the case study. In this dissertation it is the combination of approaches that have led to a greater understanding of the land use in the study area. Especially moving between empirical, inductive methods and theoretical, deductive methods has proven to be a useful approach to stimulate theory building.