Information on community structure and spatial distribution of benthic habitats are important in marine conservation and management. Coral areas, often monitored by trained scuba divers, are of importance for the ecosystem goods and services they provide. The data gathered may, however, be limited due to cost and time constraints. These restrictions and the continuing decline in coral reef health contribute to the need to develop rapid methods to efficiently document the distribution and status of coral reefs. A Rapid Assessment Instrument for Coastal Benthic Habitats (ARAICoBeH) System was developed to enable large-scale but low-cost coastal benthic habitat characterization and mapping without compromising accuracy. Inquiries on community structure and status in coral-dominated areas are also possible with the data collected using the method. The instrument, as well as the data processing and mapping algorithm are described in detail in this paper. A comparative study was conducted between ARAICoBeH and the frequently used underwater photo transect method. Variables compared were percent coral cover, functional group diversity, community structure as well as time and monetary requirements. There were no significant differences in estimates of percent coral cover and diversity of benthic functional groups for majority of sites while estimates of community structure were very similar. ARAICoBeH is cheaper and requires less time to gather the same amount of data as that of the photo transect method. The spatial distribution of coastal benthic habitats and community structure of coral-dominated areas in El Nido, Palawan, Philippines, are included to illustrate the application of the method.