S eagrass is a group of flowering plants that live in shallow sheltered areas along the UK coastline where they form dense green meadows under the sea. It is one of the most important sources of coastal primary production and it provides a critical habitat for juvenile reef fish and commercial fisheries. However, seagrass experiences numerous local and broader scale threats and is seen to be declining globally. Connectivity between populations is vital to the survival of extinction-prone plants, including those at risk from local environmental change, as well as pests and pathogens, with globally important implications for applied plant ecology. The over-arching goal of this study is to gain an understanding of the spatial population genetics of eelgrass, Zostera marina, in the Isles of Scilly, UK. The Isles of Scilly includes the largest continuous expanse of seagrass in England and Wales and is reported to be amongst the best condition in the UK. However, long term monitoring has revealed worrying declines there. Using an existing panel of 15 microsatellites, we estimated genetic variation in Zostera marina at five sites around the Isles of Scilly and compared this to long term ecological monitoring. We tested hypotheses on how long term declines in local seagrass populations are predicted to result in restricted genetic diversity and departure from Hardy-Weinberg equilibrium. As predicted, the level of genetic variation was found to be substantially lower at the two sites observed to be in long term decline. However, while all sites had less observed heterozygosity than expected under Hardy-Weinberg equilibrium, observed heterozygosity was greatest at the two declining sites, and inbreeding lowest at these two sites. This is contrary to the widely held assumption that low heterozygosity and high inbreeding are signs of poor population health and viability. We propose that the explanation for this is a shift in the relative contributions of sexual and asexual reproduction, likely resulting from the underlying causes of population decline. A collapse in vegetative reproduction through rhizome extension, leaving flowering as the main source of productivity could result in these observations. This not only has implications for understanding seagrass population viability but also wider implications for assessing numerous plant species with similar reproductive strategies.