Background Indigenous trees and shrubs play an important role in multifunctional forest management. They form a significant part of the biodiversity in our forests. Forest reproductive material (FRM) of autochthonous Flemish origin is sold under the quality label ‘Plant van Hier’, a certification mark of the Agency for Nature and Forests. To ensure the provenance of the seedlings, we developed a DNA-database of genetic profiles of potential parent trees, using species-specific genetic markers. This database enables the traceability of FRM of the ‘Plant van Hier’ label throughout the entire production chain; from seed harvesting and cultivation to planting by the end user. This database contains the genetic profiles of almost all possible parent trees present within 27 Flemish autochthonous seed orchards of eight ecologically important tree and shrub species: Carpinus betulus, Corylus avellana, Frangula alnus, Populus tremula, Sorbus aucuparia, Tilia cordata, Tilia platyphyllos, and Ulmus laevis. The profiles were established using microsatellite markers (11 to 24 markers per species). New genetic markers were developed for Carpinus betulus and Ulmus laevis. PCR products were run on an ABI 3500 Genetic Analyser (Thermo Fisher Scientific). Files The files will be updated when new genotypes are added to the seed orchards. The current data files contain data from genotypes collected in the period 2018-2023. Species_genotypes These files contain the genetic fingerprints of the parent trees of autochthonous Flemish seed orchards. Missing data is indicated as ‘MD’. For Carpinus betulus, an octoploid species, the allelic phenotype is given instead of the genotype as the number of times that an allele occurs on a specific locus is not known. The next metadata is additionally given:- Species: the Latin name of the species- Seed_orchard: the name of the seed orchard in which the genotypes are located- Code_seed_orchard: the code of the seed orchard in which the genotypes are located as given in the Register of Flemish Forest Reproductive Material (‘Register bosbouwkundig uitgangsmateriaal’; inbo.be)- Genotype: the fieldname given to the genotype- Origin: the location where the genotype was collected in Flanders, Belgium. Genotypes were collected from natural stands which are assumed to have an autochthonous origin. When the specific location is unknown, the location ‘Flanders’ is given. - Year_sampled: the year in which the genotypes were sampled in the respective seed orchard for genetic analysis. Species_binsets These files contain the binsets and allele names that are used to score the alleles of the genotypes in the programme Geneious Prime 2019.3.2 (https://www.geneious.com). For Tilia platyphyllos and Tilia cordata, the same binsets were used.