Interspecific hybridisation and gene flow from cultivated plants may have profound effects on the evolution of wild species. Considering the cultural history and past use of U. minor and U. glabra trees in Flanders (northern Belgium), we investigated the extent of human impact on the genetic variation of the remaining, supposedly indigenous elm populations. We therefore examined the rate of interspecific hybridisation, which is expected to be higher under human influence, the occurrence of clones within and among locations, the presence of cultivars and their possible offspring. Based on results produced using 385 Amplified Fragment Length Polymorphic (AFLP) markers, 46% of the 106 investigated Flemish elms appeared to be F1 hybrids or backcrosses to one of the parent species, while no F2 hybrids (F1 x F1 progeny) were found. Clonality was mainly found among U. minor and hybrids, which are more likely to form root suckers or sprouts as opposed to U. glabra. The majority of the studied locations (76% of the locations with multiple samples) showed evidence of clonal reproduction. Several, sometimes distant, locations shared a multilocus lineage. We also found indications of gene flow from cultivated elms into native species. It is conceivable that reproductive material has been moved around extensively, obscuring the natural genetic structure of the elm populations. The results help guide the Flemish elm genetic resources conservation program. ; AFLP matrix UlmusThe data file contains two spread sheets. The first shows the AFLP data - in the first column the sample codes, in the second the location codes and in the third the species. The next 385 columns represent the different markers, named according to the primer combination and fragment size. Marker presence is noted as "1", marker absence is noted as "0". The second spread sheet contains location information: location code, country, city,longitude (lon),latitude (lat), number of samples (N) and remarks. Coordinates are in decimal degrees.