The scleractinian reef building coral Madracis decactis is a cosmopolitan species. Understanding host–symbiont associations is critical for assessing the coral’s habitat occupancy and it’s response to environmental changes. In this study, we performed fine grained phylogenetic analyzes of Symbiodiniaceae algae associated with Madracis across a broad latitudinal gradient in the SW Atlantic (Abrolhos Bank, and St. Peter and St. Paul Archipelago). Previous studies have argued that Madracis is a specialist coral, with colonies harboring a single symbiont type B. However, these previous studies have not precisely addressed if Madracis is colonized by several types of Symbiodiniaceae simultaneously, or if whether this coral is a specialist. The hypothesis that Madracis is a generalist coral host was evaluated in the present study. A total of 1.9 million reads of ITS2 nuclear ribosomal DNA were obtained by Illumina MiSeq sequencing. ITS2 sequences were classified into Clades A, B, and C in Abrolhos, and only clade B symbionts recorded in St. Peter and St. Paul. This study also demonstrate that a single Madracis colony can host different symbiont types with >30 Symbiodiniaceae species. Abrolhos corals presented a higher photosynthetic potential as a possible result of co-occurrence of multiple Symbiodiniaceae in a single coral colony. Multiple clades of Symbiodiniaceae possibly confer coral hosts with broader environmental tolerance and ability to occupy diverse or changing habitats.