Sainfoin cultivation relay mainly on old varieties or on populations whose characteristics are not clearly established. Further advances in sainfoin cultivation require the characterisation of existing genetic resources, for its protection and its possible use. Along with morphological and agronomic characterisation, the use of genetic marker may increase the efficiency of this characterisation. As little have been done in sainfoin at molecular biology level, we tried to transfer microsatellites, a type of genetic markers, from related legumes species to sainfoin.The screening of 35 microsatellites from lucerne and soybean allowed us to identify 6 microsatellites that were conserved in sainfoin. The screening of a collection of European sainfoin accessions with these 6 microsatellites helped us to retrace the history of sainfoin cultivation in Europe, to identify repeated material in the collection and to establish the level of relatedness between entries. They were separated clearly from Spanish wild species and segregated in 5 groups coming respectively from Britain, Eastern Europe, France, Eastern Europe and Italy or Spain. The use of this information will be useful in the mark of further plant breeding programs as it may help to develop improved varieties with wide genetic base. It may also serve to design an effective conservation strategy as it is able to identify repeated accessions.