<p>Shaded agroforestry systems with low levels of diversity are generally conceived as having less complex structures and being dominated by species for market, while systems with greater levels of diversity are thought to have more complex structures and be dominated by species for family consumption. The present study, carried out in the southern Mexican state of Tabasco, evaluated the impact of management of diversity of cacao agroforestry systems on their structure and socioecological roles of tree species present. We carried out extensive interviews and ethnobotanical transects in cacao agroforestry systems with low and high levels of diversity in order to characterize agroecosystem management as well as uses and socioecological roles of their tree vegetation. Using the data for vegetation, we calculated a variety of indices regarding tree vegetation structure. Management, uses, and socioecological roles of vegetation were found not to vary significantly between the two levels of biodiversity. Both systems are dominated by multifunctional, multi-role species. Biodiversity is molded by the history of the systems, and by farmers’ past needs and decisions as well as their current needs. None of the structural indices calculated varied according to level of biodiversity, and yield of cacao trees was influenced only by the number of cacao trees. The low ratio between diversity and other characteristics of vegetation indicates a need to develop a more complex theory regarding the relationship between agroforestry structure and biodiversity, by which biodiversity is not the only characteristic of vegetation determining the socioecological functionality of agroecosystems.</p>