Summary Historical declines of marine megaherbivores have led to a view of seagrass communities structured largely by abiotic disturbance and plant competition. There is, however, growing recognition of the significance of top‐down control through herbivory, on seagrass ecosystem processes, raising the question of how meadows functioned under historically high populations of megaherbivores. We assess the impacts of such intense herbivory on seagrass meadow composition in the Lakshadweep islands (India), where high‐density feeding aggregations of green turtles have persisted for over a decade. We use a series of complementary approaches: (i) natural herbivory exclosures (ii) published data on seagrass composition before and after turtles established (at one atoll: Agatti) and (iii) present species composition along a turtle herbivory gradient over multiple atolls. Long‐term natural exclosures in Agatti indicated that sustained turtle grazing caused clear shifts in species dominance from the long‐lived, higher‐successional Thalassia hemprichii to the relatively short‐lived, pioneering species Cymodocea rotundata (dominant in grazed areas). T. hemprichii was the dominant species c. 20 years ago but is now restricted to areas within exclosures in Agatti, and to the least grazed meadows (<5%) in other atolls. We conducted field experiments to identify possible mechanisms by which herbivory mediated direct or apparent competitive interactions between seagrass species. To verify if grazing reduced growth rates of T. hemprichii in comparison with C. rotundata, we conducted clipping experiments in 1m2 plots, simulating turtle herbivory on equal shoot proportions of both species. After 4 months, T. hemprichii shoot density showed major declines in clipped vs. control plots, but C. rotundata shoot density remained relatively unaffected. To test whether selective grazing on T. hemprichii facilitated C. rotundata, we established paired seagrass preference experiments. Turtles had clear preferences for T. hemprichii (64%), but also grazed on C. rotundata. Synthesis. Taken together, our results show that high‐impact turtle herbivory changes seagrass composition, precipitating dominance shifts in grazed meadows by mediating direct and apparent competition. Given the crucial role of megaherbivores in seagrass meadow functioning, our results suggest that past meadows may have had natural functional limits to megaherbivore densities that they could sustainably support.