Two model legumes, Medicago truncatula (Mt) and Lotus japonicus (Lj), are currently targets of large-scale genome sequencing projects. As a result, legumes are one of few plant families with extensive genome sequence in multiple species. The prospect of integrating genome information from Mt and Lj together into a reference for legume genomics will provide exciting opportunities for plant biologists. Because the Mt and Lj sequencing efforts are both clone by clone (as opposed to shotgun or filtered genome sequencing strategies), syntenic comparisons between these two genomes and with other plant taxa will be straightforward and highly informative. Already, the Mt and Lj genome sequences offer novel insights into the organization and evolution of legumes, as well as the similarities and differences with genomes of other plant families, such as Arabidopsis (Arabidopsis thaliana; Zhu et al., 2003) and Populus trichocarpa (G. Tuskan, personal communication). A growing number of researchers are using the Mt and Lj genomes to positionally clone genes of biological importance, especially those involved in symbiosis (Schauser et al., 1999; Endre et al., 2002; Krusell et al., 2002; Nishimura et al., 2002; Stracke et al., 2002; Madsen et al., 2003; Ane et al., 2004; Levy et al., 2004). Increasingly, researchers working in broader aspects of plant biology will find the genome sequences of Mt and Lj essential to their research. In this review, we briefly describe basic features of the Mt and Lj genomes, gleaned from the growing body of genome sequence data. We compare the two genomes through direct sequence comparisons, based on a total of 122 Mb of finished (phase 3) sequence available between the two genomes. These comparisons lay a foundation for integrating knowledge about these two systems and increasing their utility as reference legumes.