Urban trees form a vital component of sustainable cities but the use of a restricted range of species and genotypes may pose a risk to global biodiversity. Despite several studies investigating tree species diversity, intraspecific genetic diversity of urban trees remains largely unexplored. Here, we characterized the genetic diversity of Tilia × europaea, one of the most widely planted urban tree species in Northwest Europe. We compared the genotypic diversity of historical plantings of Tilia spp. from the 17th century with the genotypic diversity of currently available planting stock in Belgium and the Netherlands. In total, 129 trees were sampled and genotyped with 14 microsatellite loci and 150 polymorphic Amplified Fragment Length Polymorphism markers. In Northwest Europe, homogenization of urban T. × europaea plantings already started at the 17th century. Genetic diversity within contemporary commercial planting stocks was extremely narrow and consisted mainly of two clones, sold under the name ... : AFLP dataAmplified Fragmenth Length Polymophisms (AFLP) data used for clonal assignment in the format of the program GENODIVE.VandenBroeck_BIOC2018_Tilia_AFLP.txtSSR dataSingle Sequence Repeats (SSRs) data used for clonal assignment in the format of the program GENODIVE.VandenBroeck_BIOC2018_Tilia_SSR.txt ...