The dataset comprises four files. 1) Alpujarra_Antirrhinum_species_AFLP_genotypes.txt contains amplified fragment length polymorphism (AFLP) genotypes of wild populations of five Antirrhinum species (A. barrelieri, A. rupestre, A. hispanicum, A. molle and A. tortuosum) from the Alpujarra region of southeast Spain. 2) Alpujarra_Antirrhinum_species_phenotypes.txt contains phenotype data for the same populations. 3) A.barrelieri_x_A.rupestre_F2_traits_and_genotypes.txt contains restriction-site associated DNA (RAD) genotypes and phenotype data for an F2 population of A. barrelieri x A. rupestre, the F1 parents and species grandparents. 4) Key_to_RAD_indices.txt contains the index sequences needed to assign RADseq reads to individuals. Further details are given in the ReadMe.txt file.Please see ReadMe.txt for further details of file structure.