The mission of the Legume Information System (LIS) is to facilitate discoveries and crop improvement in the legumes, which are critical components of global food and agriculture systems. LIS stores datasets from numerous legume species, and uses the reference species Glycine max, Lotus japonicus, and Medicago truncatula as a basis for comparisons between and among diverse legume species. Genomic references like pigeonpea (recently published) and others will also be added as they become available. For other legume species, LIS hosts transcriptome assemblies and other datasets. Comparative maps, reference datasets, sequence search tools, etc. make these datasets available for exploration and discovery. New features in 2011 include species-specific pages for many additional legumes, new genome browsers for Medicago and Lotus, gene family pages for legume and other species, and inferred syntenic relationships between these genomes. A new site layout offers new species pages, as well as a number of entry points for exploration by gene, trait, function, and genomic context. The LIS multi-sequence, multi-target search tool, Seqqle, serves as a portal to genome browsers at SoyBase, the JCVI Medicago truncatula Project, the Medicago HapMap Project, and Kazusa's Lotus japonicus site, and to the Medicago truncatula Gene Expression Atlas at the Noble Foundation. LIS is funded by the USDA-ARS, and is developed and maintained jointly by the National Center for Genome Resources (NCGR) and the USDA-ARS at Ames, Iowa. The team invites you to explore LIS at http://comparative-legumes.org and welcomes your comments and suggestions.