Airborne remote sensing with a CASI-550 sensor has been used to map the benthic coverage and the bottom topography of the Pulau Nukaha coral reef located in the Tanimbar Archipelago (Southeast Moluccas, Eastern Indonesia). The image classification method adopted was performed in three steps. Firstly, five geomorphological reef components were identified using a supervised spectral angle mapping algorithm in combination with data collected during the field survey, i.e. benthic cover type, percentage cover and depth. Secondly, benthic cover mapping was performed for each of the five geomorphological components separately using an unsupervised hierarchical clustering algorithm followed by class aggregation using both spectral and spatial information. Finally, 16 benthic cover classes could be labelled using the benthic cover data collected during the field survey. The overall classification accuracy, calculated on the biological diverse fore reef, was 73% with a kappa coefficient of 0.63. A reliable bathymetric model (up to a depth of 15m) of the Pulau Nukaha reef was also obtained using a semi-analytical radiative transfer model. When compared with independent in-situ depth measurements, the result proved relatively accurate (mean residual error: -0.9m) and was consistent with the seabed topography (Pearson correlation coefficient: 86%)

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