The dataset includes species richness of benthic branching and encrusting gorgonians collected from multiple habitat types across the south Florida shelf, inside and outside of the no-take management zones, and throughout the Florida Keys from south of Miami to the Dry Tortugas, from 1999 through 2009. The data set documents the branching and encrusting gorgonian species richness and changes over time of benthic coral reef organisms in the region. The data were collected during synoptic broad-scale surveys of coral reef and hard-bottom habitats that were stratified into sub-regions or along-shelf positions (e.g., Biscayne, Upper, Lower and Middle Keys, and the Dry Tortugas), resource management zones (e.g., FKNMS no-take zones and reference areas, and National Parks), and various habitat types (e.g., patch reefs, low relief hard-bottom, high-relief spur and groove, etc.). A 200m x 200m polygon grid was used to overlay onto existing bathymetry and benthic habitat maps of the study area, and a two-stage stratified random design was used to select sites for sampling from various strata combinations of cross-shelf habitat type, along-shelf position (i.e. region), and management zone (Ault et al. 2006, Smith et al. 2011). At each 200-m x 200-m site, four 15-m transects were deployed for data collection. More information on the individual projects from which data were compiled for this dataset is located online at http://people.uncw.edu/millers/index.htm.