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Our understanding of global seagrass ecosystems comes largely from regions characterized by human impacts with limited data from habitats defined as notionally pristine. Seagrass assessments also largely focus on shallow-water coastal habitats with comparatively few studies on offshore deep-water seagrasses. We satellite tracked green turtles (Chelonia mydas), which are known to forage on seagrasses, to a remote, pristine deep-water environment in the Western Indian Ocean, the Great Chagos Bank, which lies in the heart of one of the world's largest marine protected areas (MPAs). Subsequently we used in-situ SCUBA and baited video surveys to survey the day-time sites occupied by turtles and discovered extensive monospecific seagrass meadows of Thalassodendron ciliatum. At three sites that extended over 128 km, mean seagrass cover was 74% (mean range 67–88% across the 3 sites at depths to 29 m. The mean species richness of fish in seagrass meadows was 11 species per site (mean range 8–14 across the 3 sites). High fish abundance (e.g. Siganus sutor: mean MaxN.site−1 = 38.0, SD = 53.7, n = 5) and large predatory shark (Carcharhinus amblyrhynchos) (mean MaxN.site−1 = 1.5, SD = 0.4, n = 5) were recorded at all sites. Such observations of seagrass meadows with large top predators, are limited in the literature. Given that the Great Chagos Bank extends over approximately 12,500 km2 and many other large deep submerged banks exist across the world's oceans, our results suggest that deep-water seagrass may be far more abundant than previously suspected.