Coffee is one of the world's most valuable agricultural export commodities. In particular, coffee is a key export and cash crop in numerous tropical and subtropical countries having a generally favorable impact on the social and physical environment.While coffee species belong to the Rubiaceae family, one of the largest tropical angiosperm families, commercial production relies mainly on two species, Coffea arabica L. and Coffea canephora Pierre, known as Robusta. Although a considerable genetic diversity is potentially available, coffee breeding is still a long and difficult process. Nevertheless, genomic approaches offer feasible strategies to decipher the genetic and molecular bases of important biological traits in coffee tree species that are relevant to the growers, processors, and consumers. This knowledge is fundamental to allow efficient use and preservation of coffee genetic resources for the development of improved cultivars in terms of quality and reduced economic and environmental costs. This review focuses on the recent progress of coffee genomics in relation to crop improvement.