Coastal regions are widely recognised for their ecological and socio-economic importance. One of the major threats to worldwide coastal ecosystems is the introduction of non-indigenous species (NIS). In Portugal, shipping has been reported to be the most likely vector for the introduction of NIS in coastal regions that can establish and become invasive, negatively impacting native biodiversity. If prevention fails, the early detection and surveillance of NIS is essential for coordinating a timely and effective response to invasions. The aim of this project is to develop, optimize and implement DNA-based tools, particularly high-throughput sequencing (HTS), for the early detection and monitoring of NIS in Portuguese coastal waters, during 3 years of research.