The purpose of diversity analyses conducted in the Generation Challenge Programme is to provide rational access to superior alleles involved in agricultural traits for important food crops. As many as 22 crops are being considered, with very diverse biological features. A particular emphasis is given to drought tolerance. Molecular markers are at the center of this endeavour and they are expected to help: - diversify access by enlightening all components of germplasm structure, - show germplasm sections with potential linkage disequilibrium which lends itself to whole-genome scan mapping, - evaluate the degree of LD in various populations, - guide the choice of unstructured populations for association studies. Full efficiency will be reached when molecular tools have been tested, selected, adapted and made available. The first characterizations are being conducted with SSRs. Present methodological explorations are assessing the value of DArTs and EcoTILLING. Next challenges will be the application of LD mapping to populations in the course of varietal improvement and the connection of molecular correlative studies with in situ germplasm management practices. (Texte intégral)