Darwin studied domesticated plants and animals to try to understand the causes of variability. He observed that variation is greatest in the part of the plant most used by humans, but explanations of the causes of this variation had to await the discovery of Mendelian genetics and subsequent advances in the understanding of the structure and mode of action of genes, from the one gene, one enzyme hypothesis to the role of transcriptional regulators. Darwin credited his studies on domesticated plants and animals with demonstrating to him the power of selection. He recognized two forms of human-mediated selection, methodical and unconscious, in addition to natural selection. Selection leaves a signature in the form of reduced diversity in genes that have been the targets of selection and in ‘hitch-hiking’ genomic regions linked to the target genes. These so-called selective sweeps may serve now to identify genes targeted by selection in early stages of domestication and thus provide a possible guide to crop improvement in future. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161, 203–212.