Genetic assignment at different geographical levels. A case study in a forest tree species (Pinus pinaster Ait.) using SNP markers. This dataset is associated with an article that was published in Evolutionary Applications. The article's DOI is 10.1111/eva.70145. Genomic dataset comprising 10,185 SNPs from 1,579 samples of Pinus pinaster across 86 populations, 45 regions of provenance and 10 gene pools. 1) metadata of samples, 2) genotype information in nucleotide format, 3) genotype information in genepop format (compatible with assignPOP), 4) metadata including corresponding population, region of provenance and gene pool information of each sample (compatible with assignPOP), 5) genotype information in RUBIAS format, samples divided into populations and regions of provenances, 6) genotype information in RUBIAS format, samples divided into regions of provenances and gene pools.