An increasing number of plant and animal species are being introduced into Europe, whether by accident or deliberately. Some are able to establish viable populations and may outcompete local species and/or disrupt ecosystem functioning. In order to protect native biodiversity and ecosystems, and mitigate the potential impact on human health and socio-economical activities, the European Commission issued Regulation 1143/2014, listing 37 IAS. The Regulation foresees in different steps: prevention, early detection, eradication or management of established populations. Aside from compiling this species list and gathering information on presence/distribution, ecology, impacts and management, accurate methods for rapid identification are required when suspicious biological material is encountered. In cases where a morphological identification is problematic (e.g. cryptic species, trace material, early life-stages), DNA-based identifications may be an alternative method. The purpose of the present work is to investigate and evaluate the available DNA sequence databases for each IAS included in the EC Regulation. We explored the usefulness of a number of popular, publicly available DNA sequence data for identifying these IAS (e.g. COI, ITS2, rbcL, matK etc. in BOLD and GenBank). As such, we illustrate current problems with the molecular identification of the IAS due to (1) limits of COI barcodes and other DNA sequences for species identification, (2) misidentifications of voucher specimen, (3) insufficient taxon coverage of the IAS and related species, and (4) lack of adequate metadata on the reference specimens (e.g. subspecies, locality) in GenBank and BOLD.