The process of domestication has caused drastic phenotypic changes in crop plants, due to adaptation to cultivation and to the needs of the farmer. Here, we have analysed the effects of domestication and breeding in tetraploid wheat through metabolic profiling of the kernels. Using a high-throughput platform based on gas chromatography coupled with mass spectrometry, we compared the chemical composition of 12 durum wheat varieties with 11 emmer landraces and 16 Triticum dicoccoides genotypes. The kernels were obtained from a randomised field experiment with three replicates. The differences between populations and genotypes for 70 metabolites were compared with those for 520 DaRT mapped markers. There is high heritability for all of the metabolites, with a mean of 92%, and which ranges from 33% for aspartic acid to almost 100% for alanine, proline and quinic acid. All of the data were also used for QST vs FST comparisons, to determine the effects of selection during the process of domestication and breeding in durum wheat.