In the past decade, extraordinary progress has been made in the analyses of plant genomes. In contrast to plant models, research devoted to molecular characterization of coffee (Coffea L.) has been rather limited. However, several key advances in coffee molecular genetics have been achieved which could have considerable potential for improving the efficiency of conventional coffee breeding. Molecular-based investigations in coffee have concerned several (?) of research such as 1) evaluating the genetic diversity, 2) determining the genome organization and species relationships, 3) development of genetic maps, and 4) the identification of economically important genes. Progress will be briefly described and discussed in relation to coffee improvement. Major challenges for years to come and interests of international co-operation will be introduced.