The file contains genotypic data of 298 trees from 10 populations of Ailanthus altissima in eastern Austria. Samples were collected in the field and genotyped according to the methods described in the cited research. The file contains genotypes of five (5) microsatellite loci scored using fragment length analysis (Aa22, Aa69, Aa75, Aa76 and Aa82) and further twelve (12) microsatellite loci scored based on an SSR-GBS approach (loci loci HT2, HT7, HT9, HT10, HT16, HT19, HT22, HT24, HT27, HT30, HT31 and HT35). Genotypes of the same population assigned to a particular multilocus lineage (MLL) are marked with a capital letter (from A-F)