Shallow water reef-building corals associate with photosynthesizing dinoflagellates (Symbiodinium spp.) that may affect growth and resilience of their hosts. Understanding host–symbiont associations is critical for assessing the susceptibility of corals to climatic changes. Despite that, the diversity of Symbiodinium associated with corals from the Southwestern Atlantic Ocean is poorly known. Here, we describe diversity across major Symbiodinium clades associated with colonies of the endemic reef-building coral Mussismilia hispida (Verrill, 1902) along the Brazilian coast. By analyzing the 18S rDNA gene, we found that M. hispida associates with three clades of Symbiodinium (A, B and C). Moreover, the geographic distribution of host–symbiont associations is related to temperature and turbidity and closely follows previously recognized reef regions along the Brazilian coast. These results suggest that similar ecological processes are likely shaping both the reef communities and the host–symbiont associations over M. hispida distribution along the coast. Our study provides an advance in the understanding of symbiont diversity in a key reef-building coral. In addition, it contributes new insights for future investigations aiming at comprehending the factors determining Symbiodinium geographic distribution.