Azuki bean (Vigna angularis) and rice bean (V. umbellata) are locally important legumes that were domesticated in Asia. They are genetically closely related and therefore suitable for comparative genomics studies. The center of genetic diversity of azuki bean is in East Asia and it was most probably domesticated in Japan based on the archaeobotanical and genetic evidences. The center of genetic diversity and domestication of rice bean is in Southeast Asia. The domestication of rice bean involved fewer gene (QTLs) mutations with larger genetic effects than azuki bean. The distribution of major domestication genes in rice bean is limited to two linkage groups compared with five in azuki bean. In azuki bean the major domestication genes are abundantly detected on linkage group 9 (LG9), while in rice bean they were found on LG4. Surprisingly, many species specific QTLs were detected such as azuki bean’s erect stem QTL on LG9 and rice bean’s seed size increase QTL on LG4. Such species specific QTLs suggest the possibility that rice bean and azuki bean can provide novel genes for breeding. Comparative genomics among closely related species is an efficient way to find novel genes for breeding.