The Eurasian genus Medicago is best known for the perennial species M. sativa (alfalfa). Alfalfa is the world’s oldest, most important, and most intensively studied fodder crop. There is huge promise for extending the importance of alfalfa well beyond its present primary use as a feed for livestock. This species has potential uses in several domains such as: pharmaceuticals, biodegradable plastics, biofuels, textiles, and human nourishing. Medicago sativa is a polymorphic species with a variation pattern that has been complicated by hybridization and gene flow, mediated naturally or by human forces. We aim to develop a new population genomic approach to disentangle complex processes such as population divergences, migration and hybridisation/introgression among intraspecific diploid populations in a spatial and temporal framework. Specifically, this project aim to: (i) determine the genetic structure within Medicago sativa in order to characterize discrete wild genetic pools (populations) of this economically important plant species; (ii) investigate the relationships among the distinct M. sativa populations and taxa; (iii) identify geographical origin of M. sativa intraspecific taxa and the forces driving their spread; and (iv) investigate ecological adaptation in wild populations connected by gene flow in order to establish a basis for future breeding programmes.