Large-scale losses of seagrass beds have been reported for decades and lead to numerous restoration programs. From worldwide scientific literature and 20 years of seagrass restoration research in the Wadden Sea, we review and evaluate the traditional guidelines and propose new guidelines for seagrass restoration. Habitat and donor selection are crucial: large differences in survival were found among habitats and among donor populations. The need to preferably transplant in historically confirmed seagrass habitats, and to collect donor material from comparable habitats, were underlined by our results. The importance of sufficient genetic variation of donor material and prevention of genetic isolation by distance was reviewed. The spreading of risks among transplantation sites, which differed in habitat characteristics (or among replicate sites), was positively evaluated. The importance of ecosystem engineering was shown in two ways: seagrass self-facilitation and facilitation by shellfish reefs. Seagrass self-facilitative properties may require a large transplantation scale or additional measures.