In 2007 and 2008, multiple sites were identified in the Wakatobi Marine National Park, South East Sulawesi, Indonesia, which each represented a point along a gradient of light quality, temperature and turbidity. This gradient included `optimal', intermediate and marginal sites, where conditions were close to the survival threshold limit for corals. Coral communities changed across this gradient from diverse, mixed growth form assemblages to specialised, massive growth form dominated communities. The massive coral Goniastrea aspera was the only species identified at the most marginal and optimal sites. Branching species Acropora formosa and Porites cylindrica were only identified at optimal sites. The in hospite Symbiodinium community also changed across the environmental gradient from members of the Symbiodinium clade C on optimal reefs (in branching and massive species) to clade D on marginal reefs ( in massive species). Substantial variability in respiration and photosynthesis was observed in massive coral species under different environmental conditions, which suggests that all corals cannot be considered equal across environments. Studying present-day marginal environments is crucial to further understanding of future reef bio-diversity, functioning and accretion, and from work presented here, it is likely that as future climate change extends marginal reef range, branching coral diversity may decrease relative to massive, more resilient corals.