A better knowledge of factors organizing crop genetic diversity in situ increases the efficiency of diversity analyses and conservation strategies, and requires collaboration between social and biological disciplines. Four areas of anthropology may contribute to understand the impact of social factors on crop diversity: ethnobotany, cultural, cognitive and social anthropology. So far, most collaborative studies have been based on ethnobotanical methods, focusing on farmers' individual motivations and actions, but overlooking the effects of farmer's social organization per se. We analyze how social anthropology, analyzing intermarriage, residence and seed inheritance, can contribute to studies of crop genetic diversity in situ, by considering crop varieties as social objects and by designing socially based sampling strategies. Because seed exchange is built upon trust, seed systems are embedded in a pre-existing social structure and centripetally oriented as a function of farmers' social identity. The strong analogy between farmers' cultural differentiation and crop genetic differentiation; both submitted to the same vertical transmission processes, allows proposing a common methodological framework for social anthropology and crop population genetics, where the classical interaction between genetic and environmental factors, G x E, is replaced by a three-way interaction G x E x S, with "S" designating the social differentiation factors.