Marine spatial planning in Sweden is dependent on accurate, high resolution maps of species’ habitats and the connectivity between them. The EU commission has recently announced a resolution to protect 30% of European waters by 2030, and, as such, dependable models and maps of marine species’ distributions are needed. This project uses ensemble species distribution modelling to map juvenile spawning habitat for 22 species of fish in the Baltic Sea. Furthermore, using these habitat maps, connectivity maps, based on graph theory, are produced to determine essential habitat that contributes the persistence of the meta-population. The project also utilizes newly developed tools for spatial conservation planning, utilizing integer-programming, to determine the optimal location to protect to maximize connectivity and habitat coverage within marine protected areas. The project is funded by the Swedish Agency for Marine and Water Management (SwAM/HaV), with the work being undertaken by the Swedish University of Agricultural Sciences (SLU), within the Department of Aquatic Resources (SLU Aqua).