A process for mapping the benthic cover of coral reefs at selected sites in Vietnam’s coastal waters from high-spatial resolution, multi-spectral satellite data was developed and tested. GeoEye-1, IKONOS, QuickBird satellite images in Dam Mon, My Giang and Nha Trang respectively were used and field data was collected in 2009. Images were corrected for radiometric, atmospheric, and depth effects. Band combination of three atmospheric corrected bands, second band of PCA, and depth-invariant index of spectral band 1, 2 were used for supervised classification at fine level of description. Calibration and validation field data were acquired through georeferenced photo-transect method and photos were analysed for benthic cover. The overall accuracy of Maximum Likelihood, Minimum Distance to Means and Mahalanobis Distance classifiers were compared for each study site derived from the individual confusion matrix. Overall accuracy of the classified image using Maximum Likelihood classifier were higher than other classifiers in Dam Mon and My Giang, but Mahalanobis Distance classifier was highest in Nha Trang. Overall accuracy of classified image increased when reduced number of benthic classes. Variable environmental conditions, including water clarity and depth, along with reef structures were identified as main factors causing mis-classification and reducing the overall accuracy