According to Zertuche-González et al. (2009), Ulva spp. blooms, favored by oyster cultivation, are likely displacing subtidal meadows of Zostera marina in San Quintin Bay, Baja California. The authors propose a partial removal of the seaweed to reduce the risk of eutrophication and eelgrass displacement in the bay. We warn about the removal of Ulva spp. biomass by raising six arguments that emphasize the necessity of a historical and ecosystem-based management for San Quintin Bay. First, processes other than competitive exclusion by Ulva spp. blooms more likely explain changes of Z. marina subtidal meadows in the past decade. Second, there is no consistent evidence that oyster cultivation is promoting blooms of Ulva spp. and the loss of eelgrass. Third, the removal of Ulva spp. biomass is based on experiences of heavily anthropogenically eutrophic systems, while San Quintin Bay is not. Fourth, the proposed course of actions to restore eelgrass meadows ignores general historical baselines of estuarine and coastal systems by confusing what it means to be "pristine." Fifth, despite the important experimental evidence indicating strong top-down control in temperate seagrass meadows, Zertuche-González et al. (2009) underestimated the capacity of consumers in structuring dynamics of vegetated softbottom communities in San Quintin Bay. Sixth, Ulva expansa may exert positive effects on seagrass ecosystem properties and functions. Instead, we propose protection against the propagation of unsustainable practices in the bay, and the reintroduction of large consumers that are now absent in this ecosystem. An ecosystem-based analysis of the role of Ulva spp. on eelgrass dynamics is needed.