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Weigand, H. ; Beermann, A. J. ; Čiampor, F. ; Costa, F. O. ; Csabai, Z. ; Duarte, S. ; Geiger, M. F. ; Grabowski, M. ; Rimet, F. ; Rulik ; Strand ; Szucsich ; Weigand ; Willassen ; Wyler ; Bouchez, A. ; Borja ; Čiamporová-Zaťovičová ; Ferreira ; Dijkstra ; Eisendle ; Freyhof ; Gadawski ; Graf ; Haegerbaeumer ; van der Hoorn ; Japoshvili ; Keresztes ; Keskin ; Leese ; Macher ; Mamos ; Paz ; Pešić ; Pfannkuchen ; Pfannkuchen ; Price ; Rinkevich ; Teixeira ; Várbíró ; EkremScience of the Total Environment, 2019, 678 : 499-524. ArticleEffective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requiresreliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and contentquality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference librar-ies are particularly important if molecular identification tools are to be implemented in biomonitoring and re-ports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy FrameworkDirective (MSFD). Weanalysed gaps in the two mostimportant reference databases, Barcode of LifeDataSystems(BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses showthat coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups thatwere actively targeted in barcode projects (e.g.fish, true bugs, caddisflies and vascular plants) are well repre-sented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwaterdiatoms). We also found that species monitored in several countries often are represented by barcodes in refer-ence libraries, while species monitored in a single country frequently lack sequence records. A large proportion ofspecies (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results haveimplications for the future strategy tofill existing gaps in barcode libraries, especially if DNA metabarcoding is tobe used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species rel-evant to monitoring in multiplecountries should be prioritizedfor future collaborative programs. Wealso discusswhy a strategy for quality control and quality assurance of barcode reference libraries is needed and recommendfuture steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.