GBS markers at the population level were used to study the genetic structure of lucerne in a set of 395 accessions from Europe, North and South America and China. More than 100K SNP without missing data were obtained. The structure revealed a certain genetic distance between European and American accessions, with a continuous variation between these groups. Contrastingly, Chinese accessions were genetically separated from the other accessions. This analysis is an invitation to go more deeply into a phenotypic analysis of these genetic resources to exploit them in breeding.