Amazonian indigenous populations are approaching a critical stage in their history in which increasing education and market integration, rapid population growth and degradation of natural resources threaten the survival of their traditions and livelihoods. A topic that has hardly been touched upon in this context is migration and population mobility. We address this by analysing a unique longitudinal dataset from the Ecuadorian Amazon on the spatial mobility of five indigenous groups and mestizo co-residents. Analyses reveal traditional and new forms of population mobility and migrant selectivity, including gendered forms of marriage migration and rural-urban moves driven by education. These results illustrate a dynamic present and an uncertain future for indigenous populations in which rural, natural-resource-based lifeways may well be sustained but with increasing links to urban areas.