This dataset contains additional supporting files referenced by the following publication: • Kersten S, Chang J, Huber CD, Voichek Y, Lanz C, Hagmaier T, Lang P, Lutz U, Hirschberg I, Lerchl J, Porri A, Van de Peer Y, Schmid K, Weigel D, Rabanal FA. Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass. Proc Natl Acad Sci USA. Directory structure: Haplotypes_ACCase: this directory contains the two haplotypes (fasta format) inferred by pbaa (https://github.com/PacificBiosciences/pbAA ) for each of the 1,046 individuals for which it was possible to analyse the ACCase locus. Haplotypes_ALS: his directory contains the two haplotypes (fasta format) inferred by pbaa (https://github.com/PacificBiosciences/pbAA ) for each of the 842 individuals for which it was possible to analyse the ALS1 locus. Reference_genome: this directory contains the Pacbio CLR+Hi-C based chromosome level assembly (fasta file) of an Alopecurus myosuroides individual from the German herbicide-sensitive population DE01087 (Appels Wilde Samen GmbH, Darmstadt). In addition, it includes annotation files (gff format) for transposable elements and protein-coding genes. SNP_matrix: this directory contains the SNP matrix (vcf format) for the population study carried out with ddRAD-sequencing data.