This project is a cooperative effort between the National Ocean Service, National Centers for Coastal Ocean Science, Center for Coastal Monitoring and Assessment, the University of Hawaii, and Analytical Laboratories of Hawaii, LLC. The goal of the work was to develop coral reef mapping methods and compare benthic habitat maps generated by photointerpreting georeferenced color aerial photography, hyperspectral and IKONOS satellite imagery. The enhanced spectral resolution of hyperspectral and control of bandwidths of multispectral data yield an advantage over color aerial photography particularly when coral health and time series analysis of coral reef community structure are of interest. Depending on the type of instrument, a spectral imaging system can be utilized to see multiple colors from ultraviolet through the far infrared range. The AURORA hyperspectral imaging system collected 72 ten nm bands in the visible and near infrared spectral range with a 3 meter pixel resolution. The data was processed to select band widths, which optimized feature detection in shallow and deep water. Photointerpreters can accurately and reliably delineate boundaries of features in the imagery as they appear on the computer monitor using a software interface such as the Habitat Digitizer.