AbstractThe lack of top‐down control on Tripneustes gratilla, a sea urchin commonly known to graze on seagrass, and the bottom‐up control of its feeding preference, led to the overgrazing of seagrass meadows of the species Thalassodendron ciliatum in Changuu Island (Zanzibar Archipelago). The impact of overgrazing on seagrasses was assessed by mapping the presence of grazed versus non‐grazed seagrass patches in the study site, while the top‐down control on T. gratilla was assessed by measuring the abundance of its fish predators. The feeding preference and distribution of T. gratilla were characterized by calculating the electivity indexes for each seagrass species and measuring sea urchin density, respectively. Approximately half of the patches of T. ciliatum were overgrazed, while predatory fishes of T. gratilla were absent from the site. The Vanderploeg and Scavia's Relativized Electivity Index indicated that T. gratilla had a feeding preference for T. ciliatum, which was also supported by higher urchin densities within T. ciliatum dominated patches. Bottom‐up control of grazing activity was observed by quantifying and analyzing morphological, nutritional, and the chemical defense traits of the seagrass in relation to feeding preference and urchin density. Feeding was positively correlated to the seagrass tissue C:P ratio (ρ = 0.9), whereas urchin density showed no correlations. The bottom‐up control of the feeding preference and agglomeration of T. gratilla in T. ciliatum meadows, together with the lack of evidence of substantial top‐down control and the long recovery time of T. ciliatum led to the overgrazing of this species at this site. Overgrazing, therefore, was shown to be the result of multiple factors ranging from the traits of the seagrass and feeding preference of T. gratilla, to the abundance of predators in this area.