For several years, CIRAD (Centre de coopération internationale en recherche agronomique pour le développement) has invested in the genetic improvement of banana and plantain (Musa spp.) with the goal to make production, both for export trade and local consumption, more environmentally sustainable. A crossing strategy was developed to obtain triploid hybrid varieties directly from diploid plant material. Molecular tools have now been developed to support this conventional cross-breeding scheme. Molecular markers have given new insight in Musa genetic diversity, leading to a better understanding of the relationships between modern cultivars and their ancestors, thereby providing critical information for the choice of parent material. The Musa genome structure and genetic maps have been Investigated, clarifying the mating behaviour of gametes during meiosis and giving Insight in how to manage ploidy and interspecificity. Genes involved in character expression have been identified, and genome sequencing is ongoing as a result of an International effort. The development of these molecular tools provides breeders with important information to increase the efficiency of genetic improvement efforts. This paper presents how the molecular approach is actually implemented in CIRAD's breeding strategy.