Genomic data from 244 loci for 69 accessions representing the diploid Aegilops and Triticum species, as well as some diploid Hordeum species as outgroup (Dataset_S1). The associated 244 maximum likelihood gene trees in Newick format are rooted with the outgroup and branches with bootstrap values below 10 were collapsed (Dataset_S2). Raw GBS data for 57 accessions representing all diploid species from the genera Aegilops, Triticum, as well as Dasypyrum villosum and Taeniatherum caput-medusae as outgroup species (Dataset_S3).