In the present study, data showed high values of CCI (0.9 on average) in all the investigated sites and at the two depths for each site, with the most abundant category represented by healthy coral colonies (HCC). These data translate into a good health status of the reef corals in the study area (CCI > 0.8). The lowest CCI value was detected at Lihunu’s Garden, a site stressed by the nearby village with its run-off that causes sedimentation and bleaching of coral colonies, and with anchoring and transition of boats that may induce upturning of coral colonies. The other lower CCI values were detected at 9 m depth at Mangrove Forest with up turned coral colonies probably due to fishing activities, and at Batu Tartaruga with bleached coral colonies, even if few hard coral colonies were present while soft corals were dominant.