DNA barcoding - a research approach that aims to simplify species identifications and accelerate the inventory of the world’s biodiversity - is being gradually implemented worldwide, but only recently a specific framework started to be organized at the European level. Luso-AquaBarcode aims to implement DNA barcoding into aquatic biodiversity research in Portugal, thereby standing at the forefront of the activation of this approach in Europe, and acting as a model project at the European level. Given its large, diverse and rich EEZ, Portugal is an ideal country within Europe to implement this project. With the introduction of the EC’s Water Framework Directive, there will be greater demand for tools to expedite macrobenthos monitoring. This proposal also aims to prime the development of DNA barcoding-based tools for species identification in marine and freshwater macrobenthic communities. This proposal constitutes an objective capitalization of the research and management skills acquired by the fellow during his mobility programme at Bangor University, UK. Upon initiation of this project the fellow will have completed 5 years of Post-Doctoral activity, and therefore it is in an appropriate timing to start up a career as an independent academic. The fellow will be hosted by the Department of Biology at the University of Minho, Portugal, where he will be assigned to a starting academic position, and will be granted opportunity to lead his research group within the Centre for Molecular and Environmental Biology. Luso-Aquabarcode will provide the fellow with a significant head start for a swift integration in the institution and work environment while enabling him to expand current research endeavours. This will greatly contribute for the development of the fellow’s appointment into a permanent academic position. Hence, this proposal will be key for the development of a coherent professional project and to improve the fellows’ long-term career prospects.