While the worldwide production of coffee relies on a small number of cultivars with reduced diversity, wild coffee trees represent huge reserves of genetic diversity that could help to mitigate the effects of unstable climate and plant diseases, as well as modify the wealth of health-related chemicals present in the coffee seeds. This chapter describes the results of studies of coffee tree species distribution and characterization, phylogenetic relationships among coffee species and the molecular bases of coffee species diversification, as well as looking ahead to future developments in this area.