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While the consequences of losing seagrass meadows are well known, there is less information on the functional implications of changes in seagrass species composition. In this study, we use data from a long-term monitoring project in shallow lagoons on the Florida Gulf Coast to assess changes in the functional attributes of seagrass beds during a shift in seagrass species composition. We compare seagrass beds in 2 neighboring lagoons with different trends: one where the composition changed from 100% Halodule wrightii to a mixed bed with up to 60% Ruppia maritima, and one where the species composition remained unchanged. Our results indicate that the partial replacement of H. wrightii by R. maritima did not alter seagrass biomass m(-2), detrital biomass m(-2), benthic gross primary production, or benthic respiration. However, there was a small positive effect on benthic net primary production. While seagrass biomass m(-2) declined at both sites, the emergence of R. maritima increased the amount of available habitat through rapid expansion. Overall, our data suggest that shifts between 2 seagrass species with similar morphology, but different ecological strategies, may have little impact on the ecosystem services of seagrass beds in shallow coastal lagoons.