Using recent advances in indirect genetic methods applied to both adult plants and dispersed seeds, we find that the mean seed dispersal in a threatened marine foundation plant (the seagrass Zostera marina) is approximately 100-200m. We documented strong phenotypic variation and genome-wide differentiation among plants separated by less than the spatial scale of mean realized dispersal, which suggests genetic isolation by environment in response to depth-related environmental gradients. Within all meadows, the ratio of effective to census size (or Ne/Nc) approximated 0.1%, indicating that a fraction of existing plants provides the genetic variation to allow adaptation to environmental change.