Summary1. Ecological restoration assists the recovery of degraded ecosystems; however, restoration can have deleterious effects such as outbreeding depression when source material is not chosen carefully and has non-local adaptations. 2. We surveyed 23 eelgrass (Zostera marina L.) populations along the North American Atlantic coast to evaluate genetic structure and connectivity among restored and naturally recruited populations. 3. While populations along the North America Atlantic coast were genetically distinctive, significant migration was detected among populations. All estimates of connectivity (F ST , migration rate base on rare alleles, and Bayesian modelling) showed a general north to south pattern of migration, corresponding to the typical long-shore currents in this region. 4. Individual naturally recruited meadows in the Virginia coastal bays appear to be the result of dispersal from different meadows north of the region. This supports the hypothesis that recruitment into this region is typically a slow, episodic process rather than a permanent, continuous connection between the populations. 5. While natural recovery of populations that were catastrophically lost in the 1930s has been slow, large-scale seed-based restoration has been very successful at quickly restoring landscape-scale areal coverage (over 1600 ha in just 10 years). Our results show that restoration was also successful at restoring meadows with high genetic diversity. Naturally recruited meadows were less diverse and exhibited signs of genetic drift. 6. Synthesis. Our analyses demonstrate that metapopulation dynamics are important to the natural recovery of seagrass ecosystems that have experienced catastrophic loss over large spatial scales; however, natural recovery processes are slow and inefficient at recovering genetic diversity and population structure when recruitment barriers exist, such as a limited seed source. Seed-based restoration provides a greater abundance of propagules, rapidly facilitates the recovery of populations with higher genetic diversity, and when seed sources are chosen carefully protects regional genetic structure. Firstorder estimates indicated that the genetic diversity achieved by active restoration in 10 years would have otherwise taken between 125 and 185 years to achieve through natural recruitment events.