SignificanceOur study focused on the history of introgression between domesticated grapes and their European wild relative. We find evidence for a single domestication of grapevine with introgression from the wild relative to wine, but not to table, grapes. These regions are enriched for genes related to aromatic compound synthesis, suggesting that European wild grapes have been an important resource for improving the flavor of wine grapes. However, the beneficial effects of introgression carry a potential cost because introgressed regions have elevated numbers of putatively deleterious variants, which are usually maintained in a heterozygous state for this clonally propagated crop. The identification of introgressed beneficial and deleterious variants is important for genomic breeding of grapevines.