Genetic diversity in dominant primary producers can have important effects on overall ecosystem productivity. In addition, diversity can play a critical role in the response of these systems to disturbance. However, few experimental data are available to address how genetic diversity and disturbance interact to affect productivity. We conducted a factorial field experiment in which we simultaneously manipulated seagrass (Zostera marina) clonal diversity (2 levels) and disturbance intensity (3 levels) to examine their independent and interactive effects on seagrass biomass production. Z. marina is a key habitat provider and primary producer in shallow bays and estuaries, forming monospecific stands that also enhance secondary benthic production and promote nutrient cycling. Our experimental results confirm that seagrass clonal diversity enhances the response to disturbance, with polycultures out-producing monocultures at the highest level of disturbance. Interestingly, this positive effect was dependent on disturbance: monocultures had higher shoot production than polycultures in the absence of disturbance. The positive relationship between genetic diversity and disturbance response was not merely due to the presence of one highly resilient clone (i.e., the sampling effect). Rather, polyculture production was higher than expected based on the average performance of each clone in monoculture, suggesting that complementarity among clones contributes to the positive diversity-stability relationship in seagrass. These results reinforce the importance of incorporating greater genetic diversity in seagrass restoration efforts, which often exhibit lower diversity than natural populations.