Coral reefs and seagrass are natural fortress for small islands from waves and ocean currents. The spatial distribution of these benthic substrate should be known and monitored regularly. This study aims were to map existing benthic substrates on the reef flat of Bontosua Island, determine the spatial composition and develop index ratio. Benthic substrates were surveyed using geotagging technique. Their distribution were estimate using Quickbird image that was rectified and classified using ISOcluster method and validate by 240 selected photos. The seagrass were surveyed at 8 stasions to record percent cover and species composition. Depth profiles were track along 10 reef flat line segment. Bontosua Island has an elongated shape from South to Northwest. This study had produced a benthic substrate distribution map with thematic accuracy 76%. Total area able to map were 54.2 hectares. About 43% benthic substrates at Bontosua were mixture of coral rubble, seagrass and algae, 20% was mixture of rubble and algae, 16% dominated by seagrass, 13% mixture of sand and seagrass and 8% substrate were dominated by live coral. There were eight seagrass species found with average percent cover 37.2 ± 12.5 percent. The spatial ratio of live coral, seagrass and mixed substrate for West side reef flat was 2:20:49 and 1:9:9 for East side. This indicate that the distribution of benthic substrates on the West side is much wider than on the East side. This approach potentially applied to study the relationship between benthic substrate composition and the deformation of small islands.
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