We view agrobiodiversity as a social-ecological phenomenon and, therefore, an example of nature–gender relations within agrarian change, including social, economic, political and technical changes in agriculture and rural areas. As a result of the industrialization of agriculture, nature–gender relations in the field of agrobiodiversity have become characterized by separation processes such as conservation versus use or subsistence versus commodity production. We argue that the sustainable development paradigm, as currently implemented in European Common Agricultural Policy through the concept of multifunctionality, does not necessarily overcome separation tendencies and lead towards integration, despite its claim to bring together different ecological, economic and social needs. In our paper we critically reflect this observation and develop a theory-based analytical framework at the interface of nature and gender relations. For analytical purposes we distinguish between three different agrarian structures (pre-industrialized, industrialized and multifunctional) and focus on the development of two separation tendencies within them and their effects on agrobiodiversity. Concerning nature, we discuss the effects of separating agrobiodiversity conservation and use. With regard to gender, we discuss the separation of subsistence and commodity production. Against this background, we claim for new rural economic rationalities characterized by processes whose qualitative, material and value dimensions maintain agrobiodiversity.