Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation1. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species2.Medicago truncatulais a long-established model for the study of legume biology. Here we describe the draft sequence of theM. truncatulaeuchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ∼94% of allM. truncatulagenes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping theM. truncatulagenome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, theM. truncatulagenome experienced higher levels of rearrangement than two other sequenced legumes,Glycine maxandLotus japonicus.M. truncatulais a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, theM. truncatulagenome sequence provides significant opportunities to expand alfalfa’s genomic toolbox.