Crop seed exchange networks, shaped by social dynamics, strongly influence the organization and breadth of plant diversity in human-managed environments. Integrating an urban and market perspective, this study explores the diversity dynamics of a socio-economically important Central African fruit tree species, the African plum tree. Tree owners in urban, peri-urban and rural sites use seeds from different origins as their main propagation material, leading to locational variations in genetic diversity and structure. This analysis contributes toward building a framework to inform the research agenda of cultivated African fruit trees, by highlighting the important role of urban centers in safeguarding crop genetic resources.