Remote sensing technology is reliable in identifying the distribution of seabed cover yet there are still challenges in retrieving the data collection of shallow water habitats than with other objects on land. Classification algorithms based on remote sensing technology have been developed for application to map benthic habitats, such as Maximum Likelihood, Minimum Distance, and Support Vector Machine. This study focuses on examining those three classification algorithms to retrieve information on the benthic habitat in Pari Island, Jakarta using visual interpretation data for classification, and data field measurements for accuracy testing. This study used five classes of benthic objects, namely sand, sand-seagrass, rubble, seagrass, and coral. The results show how the proposed approach in this study provides an overall good classification of marine habitat with an accuracy produced 63.89–81.95%. The Support Vector Machine algorithm produced the highest accuracy rate of about 81.95%. The Support Vector Machine algorithm at a very high spatial resolution is considered to be capable of identifying, monitoring, and performing the rapid assessment of benthic habitat objects.