Understanding agriculture in tropical landscapes is an interdisciplinary task, focusing the interest of the ecological, physical and social sciences. Reporting on results of a long-term collaborative study of Lakandon Maya agroforestry, I review our recent insights into successional processes and the genesis of anthropic soil under Maya management. Milpa, a multicropping system centered on maize with a range of many companion crops is the axis of traditional Maya resource use. Intervention in the early stages of regeneration after cycles of maize swidden cultivation ensures the rapid recovery of original woody vegetation, enriched by species valued by humans. Maya farmers and forest ecologists have approached the tropical environment in similar ways, identifying and working with functional groups of woody species, to enhance biodiversity and ecosystem resilience. Planting or encouragement of selected tree species and the judicious use of low- intensity fires, help create anthropic soil of high organic matter and nutrient content, similar to the dark earths observed in Amazonia. The knowledge and skill revealed in Maya milpa agroforestry are invaluable tools for conservation of tropical biodiversity.