Who domesticated the crops we eat? When and where? What happened after domestication? How did crops spread across the world? These are the questions that have fascinated archaeologists for a long time. Using modern genomics techniques, we aim to answer these questions from a different angle. In mung bean (Vigna radiata), we uncovered a unique route of post-domestication range expansion. This route cannot be explained simply by human activities alone; instead, it is highly associated with the natural climates across Asia. We showed how the trans-continental climatic variability affected the range expansion of a crop and further influenced local agricultural practices and the agronomic properties of mung bean varieties. In adzuki (Vigna angularis), we obtained solid evidence of its domestication in Japan, most likely by the Jomons. We identified and validated the causal mutations for the seed coat color change during domestication. Contrary to the common belief that important yield-ensuring phenotypes (e.g., loss of pod shattering) should be selected early during domestication, we revealed a unique order of domestication trait evolution that cannot be observed from archaeological records directly.