The zoning plan for the Florida Keys National Marine Sanctuary (FKNMS) established 23 relatively small no-fishing zones distributed mostly along the offshore reef tract in 1997. In 1999, a two-stage, stratified random sampling design based on the proportion of coral reef and hard-bottom types within the FKNMS was conducted. Our study focused on differences in coverage, density, and condition of benthic organisms with respect to habitat type, regional variations, and differences between no-fishing zones and reference sites at 80 locations spanning 200 km. Most variables exhibited significant spatial differences by habitat type or between individual no-fishing zones and reference sites (e.g. species richness, coral density, gorgonian density, and recruitment), although some regional differences were also apparent. Many of the differences among the no-fishing zones and reference sites reflect the placement of the zones in well-developed offshore reefs, and for many of the variables targeted, individual zones are as different from one another as from reference sites. These results emphasize the need to address spatial variations at multiple scales, and to consider a range of variables beyond common metrics such as coral cover
