To halt the loss of biodiversity, collaboration among scientists, managers and decision makers is vital. Although biodiversity loss is a global problem, management actions influencing diversity are often on a local to regional scale. Our study is an example of a regional conservation genomic assessment developed in collaboration between scientists and managers. We used 2bRAD sequencing to assess 18 eelgrass (Zostera marina) meadows in northwestern Sweden, an area that has experienced large losses of eelgrass since the 1980s. Genetic diversity was comparable to other assessed meadows in the Atlantic, but an order of magnitude lower than eelgrass in the Pacific. All but one meadow showed high rates of sexual reproduction. Almost all meadows were divergent but grouped into five genetic clusters. Four of the clusters correspond to geographic regions that can be used to define management units. Meadows in areas with a high decline in eelgrass between the 1980s to 2020s are more inbred than meadows in areas with an increase in eelgrass. Overall, our results indicate that striving to protect a number of large eelgrass meadows within each genetic cluster is important for maintaining genetic diversity and connectivity of eelgrass in northwestern Sweden and is likely beneficial for the wider ecosystem. We estimate current indicators and essential biodiversity variables and discuss their challenges in marine facultative clonal species. We showcase how regional-scale conservation genomic assessments can serve as a foundation for protection and restoration of a priority species.