Adzuki bean (Vigna angularis) is an important legume crop, and is grown in more than thirty countries of the world. The seed of adzuki bean, as an important source of starch, digestible protein, mineral elements and vitamins, is widely used in a variety of foods for at least a billion people. Here, we generated a high quality draft genome sequence of adzuki bean by whole genome sequencing. The assembled contig sequences reached to 450 Mb (accounting for 83% of the genome) with an N50 of 38 kb, and the total scaffold sequences were 466.7 Mb with an N50 of 1.29 Mb. Of them, 372.9 Mb of scaffold sequences were assigned to the 11 chromosomes of adzuki bean using a single nucleotide polymorphism genetic map. A total of 34,183 protein-coding genes were predicted. Functional analysis revealed that significant differences in starch and fat content between adzuki bean and soybean were likely due to transcriptional changes, rather than copy number variations, of the genes related to starch and oil synthesis. We detected strong selection signals in domestication by the population analysis of 50 accessions including 11 wild, 11 semi-wild, 17 landraces and 11 improved varieties. Our analyses illuminated that the semi-wild accessions had closer relationship to the cultigen accessions than the wild type, suggesting that the semi-wild adzuki bean might be a preliminary landrace and play some roles in the adzuki bean domestication. The genome sequence of adzuki bean will facilitate the identification of agronomically important genes, and accelerate the improvement of adzuki bean. In summary, our results provide insight into evolution and metabolic differences of legumes.