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In this study we analysed: (1) the biodiversity conservation capacity of Agroforestry Systems (AFS) in temperate highlands of the Tehuacán–Cuicatlán Valley, Central Mexico, (2) human cultural motives and actions for conserving such diversity and (3) problems endangering that capacity. We evaluated the richness and diversity of perennial plant species maintained in AFS through vegetation sampling of 14 agricultural plots and compared their composition with that of natural forests (14 plots of 500� m² each). We examined the situations among communities of Náhuatl, Ixcatec and Cuicatec people, documenting through interviews the management practices of plant species and the whole system, reasons why people maintain vegetation cover within AFS, and factors influencing changes in decisions favouring agriculture intensification. In the AFS studied we recorded a total of 79 species of trees and shrubs, 86� % of them being native species and representing 43� % of all species of trees and shrubs recorded in the sampling of the natural forests the AFS derive from. People leave standing on average a total of 40 individual trees and shrubs per agricultural plot. Reasons for leave plant species standing were more frequently associated with their use as fruit trees, firewood, shade, beauty, respect to nature and other environmental benefits. Water availability for irrigation, land tenure, and dependence on agriculture and forest for peasant's subsistence were main decision factors influencing AFS variation in their composition. AFS in temperate zones are important reservoirs of biodiversity and biocultural heritage and should be keystones for conservation policies in the Tehuacán–Cuicatlán Valley.