The positive effect of mycorrhizas on plant growth and health results from a complex, molecular dialogue between the two symbiotic partners. This starts before the physical contact between plant and fungus occurs, then develops and amplifies with their morphofunctional integration and continues all along the life of the plant. Because of this dialogue, symbiosis development depends not only on the genetic make-up of both partners (Gianinazzi-Pearson and Gianinazzi, 1989), but also on environmental conditions which allow optimal coordination in their functioning (Smith and Gianinazzi-Pearson, 1988). Identifying the molecules and genes involved in the symbiotic dialogue is therefore essential not only for improving agroforestry management practices for better plant growth and health, but also for monitoring fungal development and fruit-body production. In this paper we discuss present knowledge about molecules and genes involved in mycorrhiza functioning, taking examples from the most widespread type of root symbiosis, the arbuscular mycorrhiza (Harley and Smith, 1983).