Marine spatial planning and marine protected areas (MPAs) are tools to protect biodiversity, including genetic variation. Strategies for spatial planning and for designing MPAs depend on the population structure of the species in target.
One big metapopulation...
If individuals or propagules can migrate between populations, connectivity is high resulting in a metapopulation that share a common (large) gene pool. However, if disperal links between populations are broken and connectivity restricted, for example when a habitat becomes fragmented due to human activities, the result will be isolated, small populations and loss of genetic diversity.
... or several small populations
On the other hand, sometimes populations can be genetically unique with no or little contact with others. Such populations might have evolved adaptations to local conditions and are valuable for protection. In the Baltic, many species are locally adapted to the low salinity and due to low connectivity genetically distinct from populations in the North Sea.