As a perennial crop, faster breeding methods are needed for coffee to be able to cope with the challenges of climate change that lie ahead. This chapter focuses on the state of the art of developed molecular tools, characterized traits, quantitative trait loci and candidate genes already described for Coffea canephora (Robusta coffee), which accounts for a third of the worldwide coffee production. The chapter examines coffee’s molecular markers, genetic diversity and the current state of molecular breeding, as well as looks ahead to future developments in this area.