A benthic habitat polygon coverage has been created of the coral reef ecosystem within the U.S. Coral Reef Task Force Watershed Partnership Initiative Kaanapali priority study area and the State of Hawaii Kahekili Herbivore Fisheries Management Area, West-Central Maui, Hawaii. Polygons were hand-digitized from visual interpretation of QuickBird-2 satellite imagery (2005), and SHOALS bathymetry data. We also utilized in situ knowledge from underwater photography and videography (2002-2011), side-scan sonar data, and diver and snorkeler observations. The polygons have attributes for Main Structure/Substrate, Dominant Structure/Substrate, Major Biological Cover, Percent of Major Biological Cover, Reef Zone, Unique ID, and measurements of Area (in square meters) of each polygon.