Sea otters (Enhydra lutris) and eelgrass (Zostera marina) have co-evolved along the north Pacific Rim since at least the middle Pleistocene (~600,000-700,000 years ago). When sea otters were hunted to near-extinction during the 18th and 19th century maritime fur trade, their ecological interactions were lost from nearshore communities. As sea otters have recovered in some areas, scientists have shown that otters can initiate a trophic cascade in eelgrass communities: by limiting crab abundance and indirectly releasing small grazers from crab predation, otters reduce eelgrass epiphytes, supporting eelgrass photosynthesis and biomass. While much work on otters has focused on invertebrate limitation, we have also found that in British Columbia, recovering sea otters support genetically diverse eelgrass meadows through a disturbance pathway. By excavating clams and other infaunal prey in eelgrass meadows, sea otters affect eelgrass reproductive strategies, increasing eelgrass genetic diversity. We infer that this interaction between otters and eelgrass has been important to eelgrass resilience for more than half of a million years, during shifts in coastal ice-cover and climate regimes. Sea otter recovery thus shows how evolutionarily important species interactions can be restored to sustain ecological communities today.