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In Mexico, extensive production systems have caused a drastic reduction in tropical forests and in biological diversity. Most of the agroforestry systems (AFS) in Mexico use leguminous species that naturally associate with arbuscular mycor rhiza fungi (AMF) and bacterial nitrogen fixing that aid the uptake of N and P in poor soils of the tropics. The AMF and bacteria are predominant in tropical agroecosystems with wide ranges of hosts with potential to increase growth in forest species and in crop yield. Mexico is considered one of the countries with high diversity of plants within the countries of America with potentially high number of AMF species and bacteria in different SAF. Although we have considerable knowl edge of the plants used in different AFS, the richness of soil microorganisms has received little attention in Mexico’s tropics. Understanding of the structure and functional diversity of AMF and bacteria have allowed us to generate the bases for a sustainable AFS, increasing productivity and, at the same time, AFS work as reservoirs and biological corridors that could reduce degradation of forests. Inglés