A pandemic wasting disease coupled with a destructive hurricane in the1930s, caused the local extinction of eelgrass (Zostera marina) in the Virginia coastal bays. Small patches of naturally-recruited seagrass were noticed in the late 1990s, prompting a large-scale restoration effort using seeds from nearby Chesapeake Bay. Restored meadows are currently thriving and expanding; however, there is a concern about the genetic structure of these meadows. Both large-scale die-backs and restorations are known to decrease genetic diversity, and low genetic diversity is correlated with decreased plant fitness and reduced resistance to disturbance. We conducted a broad-scale survey and used microsattelite analyses to describe the genetic diversity of the Virginia coastal bay seagrass in relation to healthy meadows along the East Coast of the United States. There was a general trend for both allelic richness and heterozygosity to increase from North to South towards the geographical margin of the plant’s distribution. Both the natural and restored meadows in the Virginia coastal bays fit this trend with no reductions due to bottlenecks or restoration founder effects. Natural recruitment into the area is from Chincoteague Bay to the North via metapopulations. Since these meadows appear to be exchanging genetic material over long distances, metapopulation dynamics should be considered in restoration site selection.