About 12,000 years ago in the Near East, humans began the transition from hunter-gathering to agriculture-based societies. Barley was a founder crop in this process, and the most important steps in its domestication were mutations in two adjacent, dominant, and complementary genes, through which grains were retained on the inflorescence at maturity, enabling effective harvesting. Independent recessive mutations in each of these genes caused cell wall thickening in a highly specific grain “disarticulation zone,” converting the brittle floral axis (the rachis) of the wild-type into a tough, non-brittle form that promoted grain retention. By tracing the evolutionary history of allelic variation in both genes, we conclude that spatially and temporally independent selections of germplasm with a non-brittle rachis were made during the domestication of barley by farmers in the southern and northern regions of the Levant, actions that made a major contribution to the emergence of early agrarian societies. Display omitted •Wild barley spikes are brittle at maturity due to thin cell walls at rachis nodes•This characteristic evolved by duplication and neo-functionalization of two genes, Btr1 and Btr2•During domestication, deletions in Btr1 or Btr2 converted the rachis to non-brittle•The deletions happened twice: first in the South (btr1) and then in the North Levant (btr2) Spatially and temporally independent selections of seeds with a non-brittle rachis were made during the domestication of barley by farmers in the southern and northern regions of the Levant, actions that made a major contribution to the emergence of early agrarian societies.