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Among the remaining tropical forests of lowland Latin America, many are inhabited by indigenous peoples, and the sustainability of their land uses is a point of heated debate in the conservation community. Numerous small-scale studies have documented changes in indigenous land use in individual communities in the context of expanding frontier settlements and markets, but few studies have included larger populations or multiple ethnic groups. In this paper we use data from a regional-scale survey of five indigenous populations in the Northern Ecuadorian Amazon to describe their agricultural land use practices and investigate the factors that affect those practices. We find the areas cultivated by indigenous households to be small compared to those of nearby mestizo colonists, but a large proportion of indigenous cultivated area is in commercial land uses. We also construct multilevel statistical models to investigate the household and community-level factors that affect indigenous land use. The results reveal significant influences on cultivated area from contextual factors such as access to markets, oil company activities, and the land tenure regime, as well as from household characteristics such as demographic composition, participation in alternative livelihood activities, and human, social and physical capitals. Overall the results are most consistent with market integration as an underlying driver of land use change in indigenous territories of the study area.