Coffee production relies on two species, Coffea arabica and C. canephora, grown in Latin America, Africa and Asia, but up to 126 species have been described in the Coffeae tribe. Traditional cultivars of the main cultivated species - C. arabica - derive from two narrow genetic bases and consequently present a homogeneous agronomic behavior characterized by high susceptibility to many pests and diseases. The low genetic diversity displayed by wild C. arabica genotypes has considerably limited the success of breeding programs based on intraspecific hybrids. Therefore, breeders have focused on the transfer of traits from other species. To date, C. canephora has been the main source of resistance traits not found in C. arabica and few species have been involved in breeding programs. However, the coffee genetic resources represent valuable sources for introducing new traits in cultivars of both cultivated species since the genome of coffee species presents strong affinities, allowing production of interspecific hybrids. This chapter summarizes available information on taxonomy, biology including geographical distribution and habitat, evolution and conservation of coffee species. The recent results achieved in studying coffee genomes are also presented here as well as the genomic resources that have been developed worldwide. The role of wild coffee in breeding programs is described considering the use of wild C. arabica as cultivars or parents of F1 hybrids, and the use of other species as donors of alien genes. The transfer of desirable genes into C. arabica cultivars can be efficiently controlled using molecular marker-assisted selection. The advent of large-scale molecular genomics will soon provide access to previously inaccessible sources of genetic variations that could be exploited in breeding programs.