This mini review examines the habitat connectivity and effectiveness of Korean Marine Protected Areas (MPAs) in the Yellow Sea Large Marine Ecosystem (YSLME) region. We first reemphasize that the Korean region of the YSLME is a single ecosystem (ecoregion) given the biophysical distribution patterns. The MPAs within the YSLME contribute about 50% to the total MPAs in Korea, accounting for about 10% of the territorial sea waters of Korea and 20% of the waters of YSLME on the Korean side. By area, national parks account for nearly 45% of the MPAs, followed by the wetland protected areas at 25%, with other types of MPA comprising the remaining 30%. Large MPA (> 100 km²) is the dominant type of MPA, accounting for 90% of the total area. We find that MPAs in the region are connected physically and perhaps also genetically. However, the level of protection was found to be low, and a no-take zone is rarely implemented. In addition, interrupted freshwater discharge caused by river-mouth dams poses a major hindrance to the physical connectivity of the MPAs. Restoration of the river-mouth dams and strengthened regulation on MPAs, with further expansion of MPAs in line with the current development of post-2020 global biodiversity frameworks, should be priorities for better management of marine resources. The newly revised law incorporating the concept of “Marine Ecosystem Axis Management” would reinforce the processes, and their effectiveness together with overall management of MPAs in Korea should be evaluated by designing appropriate measurement tools.