Crop domestication can be considered a model system of plant evolution. Genome analyses of rice have revealed the fine population structure of this major crop associated with local origins of landraces. Recent cloning of rice domestication-related genes and identification of the responsible functional nucleotide polymorphisms in landraces, while taking into account their population structures, have revealed the existence of historical signatures of the DNA involved in the domestication process. These signatures imply the importance of multiple selection steps wherein natural variants were combined to improve crop performance during domestication. These analyses will provide new insights into the relationship between Darwinian selection for agronomical phenotypes and DNA changes in terms of plant evolution.