The current biodiversity crisis calls for conservation measures that limit the negative human impact on important habitats and sensitive wild populations. To effectively protect biodiversity at all levels, including intraspecific diversity, conservation measures should be aligned with the connectivity and genetic structure of wild populations. In this review, we synthesise scientific literature on the connectivity and population structure of marine species in the Skagerrak - a marginal sea in the northeast Atlantic Ocean. We discuss the results in relation to the current management practices in the region, as well as the general transferability of our findings. The Skagerrak is one of the most intensively studied regions within this research field, and our findings show that the overall connectivity with adjacent seas is high, but asymmetric, for most species. Simultaneously, most species have populations in the Skagerrak distinct from both each other, and those in adjacent seas. Most of this population structure is associated with the convoluted Skagerrak coastline - population structure is common both among coastal populations and between coastal and offshore populations. In many mobile species, multiple populations are temporally sympatric in certain areas, but retain their genetic divergence through natal homing or other barriers to gene flow. The presence of population structure despite high connectivity is a challenge for area-based protection measures, and calls for temporally flexible management that also monitors intraspecific genetic diversity on multiple timescales.