Ectomycorrhizal symbioses involve roots of trees and soilborne fungi, which interact to create mutualistic interactions beneficial for both partners. This chapter gives an overview of the signalling pathways, molecules and secreted proteins required for the ontogenesis of such a remarkable symbiosis. Moreover, it explains how rising of next-generation sequencing technology was used as an onset for functional studies. Notably, discovery of mycorrhiza-induced small secreted proteins, key players for symbiosis development, sheds light on a sophisticated molecular dialogue used by ectomycorrhizal fungi to control its plant host and set up this belowground symbiosis.