DNA barcoding is based on the observation that species can be distinguished and identified using a short gene sequence, standardised for each of the main branches of life. Ideally DNA barcode sequences act as a proxy for species identifications, something only expert taxonomists could previously do. As a result, ecologists, population biologists, ecosystem scientists, government officials and others are now able to conduct their research with a high degree of confidence in species identifications. Barcoding is also proving to be a breakthrough for the study of poorly known taxonomic groups that were impenetrable to the taxonomist’s traditional approaches. Taken together, barcode data provide a new tool for addressing both academic research questions in evolutionary biology and ecology, and practical problems that face society. The lack of a simple, democratic and sensitive species reference system is costing society daily, i.e. pathogens, disease vectors, agricultural pests or invasive species that are not identified properly or fast enough can cause great risk and, in addition, without proper monitoring we may be ignorant of many of the ongoing biological consequences of global climate change. We propose to establish a European species reference system, using an approach that will cut the costs by up-scaling and centralising the production of reference data, while at the same time providing a basis for molecular-based biodiversity monitoring in areas relevant for conservation. Europe is well positioned to assume a leadership role in the DNA barcoding movement and to reap its benefits. Europe’s natural history museums, herbaria, and botanical gardens, taken collectively, are the world’s greatest repository of biological specimens. Several EC projects are integrating these treasure-troves of potential DNA barcode data, and an EC Network of Excellence is currently developing Europe’s ability to better exploit its collections and open up ensuing data to users for further analysis and interpretation.