Coral reefs have experienced extensive degradation across the world over the last 50 years as a result of a variety of stressors operating at a range of spatial and temporal scales. In order to assess whether declines are continuing, or if reefs are recovering, detailed baseline information is required from across wide spatial scales. Unfortunately, for some regions this information is not readily available, making future reef trajectories difficult to determine. Here we characterized the current benthic community state for coral reefs in the Wakatobi region of Indonesia, one of the most biodiverse marine regions in the world. We surveyed 10 reef sites (5, 10 and 15 m depth) to explore spatial variation in coral reef benthic communities and provide a detailed baseline. Previous data (2002–2011) were available for coral, sponges, algae and soft coral at six of our study sites. Using this information, we determined if any changes had occurred in dominance of these benthic groups. We found that benthic assemblage composition differed significantly over relatively small spatial scales (2–10 km) and hard coral cover was highly variable, ranging from 7–48% (average 19.5% ± 1.5 SE). While coral cover appears to have declined at all sites where data were available since 2002, we found little evidence for widespread increases in other benthic groups or regime shifts. Our study provides a comprehensive baseline dataset for the region that can be used in the future to determine rates of change in benthic communities.