Recent micro-economic studies of in situ conservation of crop diversity focus on competition between modern and traditional varieties of major food crops. Our paper offers a different, crop system, approach and a limited-dependent variable econometric technique to model in situ conservation of both intra- and infra-species crop diversity in a context of heterogeneous ecological and market environments, using unique household-farm data from Mexico. Our findings reject separability and indicate that market integration significantly reduces crop diversity. They underline the importance of studying diversity in the context of larger cropping systems and economic environments.