In this review, we discuss the development of molecular genetics and genomics that has allowed one to identify and characterize some of the key genes involved in cereal domestication. The list is far from being complete, but the first conclusion that can be drawn from the published works is that only a few loci have been the target of human selection in the first stages of the domestication process at the late neolithic. Mutations at these few loci have led to dramatic changes in plant morphology and phenology, transforming a wild into a cultivated plant. We also show that in the case of rice, for which the complete genome sequence is available, the development of new molecular markers based on retrotransposon insertion polymorphisms helped to resolve some of the questions regarding the origin of the domestication of the crop in Asia.