Background The Baltic Sea subpopulation of harbour porpoise (Phocoena phocoena) is small and has been drastically reduced in recent decades. The species is listed in Annexes II and IV of the Habitats Directive as well as in the national red lists of several Member States. This, in combination with a complex of threats and problems that are still fairly poorly understood, especially with reference to potential cumulative impacts, necessitates the need for improved methodologies for collecting data on population size and range, and its fluctuation over time. Objectives The overall aim of the project is to apply a best practice methodology to provide data for the reliable assessment of the distribution and habitats of the Baltic Sea subpopulation of harbour porpoise (Phocoena phocoena). This should enable the designation of sites of Community importance (SCIs) for the endangered species within the Natura 2000 network, and also provide other relevant mitigation measures. Specifically, the project aims to: Estimate densities, produce distribution maps and estimate numbers of harbour porpoises in the depth range of 5-80 m within the project area in the Baltic Sea (approximately south of latitude 55° 50’ N and east of longitude 12° E in the east, and south of latitude 60°20’N in the north). Data and maps will be produced by season for the whole study area, and possibly by country waters, if feasible; Identify possible hotspots, habitat preferences, and areas with higher risk of conflicts with anthropogenic activities for the species. In Swedish waters, the project will use these results to identify appropriate areas for protection, and within these areas, suggest appropriate management of anthropogenic activities with known or potential negative impact; Increase knowledge of the species in the nations bordering the Baltic Sea and within the EU; Implement best practice methods for cost-effective, large-scale surveillance of the species in a low density area.