Traditional agricultural and pastoral landscapes are not only crucial for the livelihoods of farmers and herders, but also provide habitat for wild biodiversity, maintain water and soil resources, and serve as the genetic basis for the global food supply. In the highlands of Ethiopia, traditional agricultural landscapes are inherently social-ecological; environmental, economic, political, and cultural forces interact to shape the extent and distribution of biodiversity and ecosystem services. By overlaying ecological and social science datasets, it becomes possible to identify emergent patterns and that are not evident when looking through a strictly disciplinary lens, and that may be crucial for effective conservation. In the Gamo Highlands of Ethiopia, the joint use of conservation genetics and farmer interviews illuminates the way in which social institutions shape the spatial dynamics of crop genetic diversity in patterns that would not be visible through genetic methods alone.