This biogeographic characterization is a project formed from the Office of National Marine Sanctuaries – National Centers for Coastal Ocean Science Long-term Agreement. This agreement originates from the common belief of these two programs within NOAA’s National Ocean Service that it is critical to have incorporated the best available science when making management decisions regarding our nation’s coastal waters. This statement is echoed as each sanctuary undergoes a revision process to their management plans. The revision process evaluates the degree to which each sanctuary meets its goals and allows an opportunity for the public to determine if there are new directions or issues they feel the sanctuary should address. The need for ecosystem based management informed by an adequate understanding of sanctuary living marine resources is consistently raised as a pressing issue in this process. The current document is one of a series of such projects aimed at providing sanctuary managers critical information on the distribution of those resources relevant to the regions they manage. This NOAA Technical Memorandum focuses on providing a spatial and quantitative characterization of the fish communities associated with the coral cap regions of the Flower Garden Banks National Marine Sanctuary. Also included, is a characterization of associated benthic habitats and sections detailing sampling design, methods and the creation of a habitat map essential in selecting sampling strata.