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ABSTRACT Species conservation and management benefit from precise understanding of natural patterns of dispersal and genetic variation. 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 eelgrassZostera marina) is approximately 100–200 m. This distance is surprisingly more similar to that of wind‐dispersed terrestrial seeds (~10s to 100s of meters) than the passive dispersal of marine propagules via currents (~10s to 100s of kilometres). Because nearshore marine plants likeZosteraare commonly distributed across strong selective gradients driven by bathymetry (depth) even within these restricted spatial scales, seeds are capable of dispersing to novel water depths and experiencing profound shifts in light availability, temperature and wave exposure. We documented strong phenotypic variation and genome‐wide differentiation among plants separated by approximately the spatial scale of mean realised dispersal. This result suggests genetic isolation by environment in response to depth‐related environmental gradients as one plausible explanation for this pattern. 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. Our results suggest that successful conservation of seagrass meadows that can adapt to microspatial and temporal variation in environmental conditions will be low without direct and persistent intervention using large numbers of individuals or a targeted selection of genotypes.