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Natural resource managers clamor for detailed reef habitat maps for monitoring smaller scale disturbances in reef communities. Coastal ocean color remote sensing techniques permit benthic habitats to be explored with higher resolution than ever before. The objective of this research was to develop an accurate benthic habitat map for an area off the northwest coast of Roatan Island, Honduras, using high-resolution multispectral IKONOS data. Atmospheric (Rayleigh and aerosol path radiance) and water column corrections (water depth and water column attenuation) were applied to the imagery, making it a robust method for mapping benthic habitats. Water depth for each pixel was calculated based on a site-specific polynomial model. A mechanistic radiative transfer approach was developed that removed the confound effect of the water column (absorption and scattering) from the imagery to retrieve an estimate of the bottom reflectance (albedo). Albedos were ≤ 12% for seagrass benthos, 12% to 24% for coral areas, and ≥ 24% for sand-dominated areas. The retrieved bottom albedos were then used to classify the benthos, generating a detailed map of benthic habitats, followed by accuracy assessment.