The rapid decline of shallow coral reefs has increased the interest in the long-understudied mesophotic coral ecosystems (MCEs). However, MCEs are usually characterised by rather low to moderate scleractinian coral cover, with only a few descriptions of high coral cover at depth. Here, we explored eight islands across French Polynesia over a wide depth range (6 to 120 m) to identify coral cover hotspots at mesophotic depths and the co-occurrent biotic groups and abiotic factors that influence such high scleractinian cover. Using Bayesian modelling, we found that 20 out of 64 of studied deep sites exhibited a coral cover higher than expected in the mesophotic range (e.g. as high as 81.8 % at 40 m, 74.5 % at 60 m, 53 % at 90 m and 42 % at 120 m vs the average expected values based on the model of 31.2 % at 40 m, 22.8 % at 60 m, 14.6 % at 90 m and 9.8 % at 120 m). Omitting the collinear factors light-irradiance and depth, these ‘hotspots’ of coral cover corresponded to mesophotic sites and depths characterised by hard substrate, a steep to moderate slope, and the dominance of laminar corals. Our work unveils the presence of unexpectedly and unique high coral cover communities at mesophotic depths in French Polynesia, highlighting the importance of expanding the research on deeper depths for the potential relevance in the conservation management of tropical coral reefs.