Coral reefs are at risk due to events associated with human activities, which have resulted in the increasing occurrence of coral diseases. Corals live in symbiotic relationships with different microorganisms, such as cyanobacteria, a very important group. Members of the phylum Cyanobacteria are found in great abundance in the marine environment and may play an essential role in keeping corals healthy but may also be pathogenic. Furthermore, some studies are showing a rise in cyanobacterial abundance in coral reefs as a result of climate change. The current study aimed to improve our understanding of the relationship between cyanobacteria and coral health. Our results revealed that the cyanobacterial genus GPI (Anabaena) is a possible opportunistic pathogen of the coral species Millepora alcicornis in the South Atlantic Ocean. Furthermore, the bacterial and microeukaryotic profile of healthy, diseased, and post-disease (skeletal) regions of affected coral indicated that a microbial consortium composed of Anabaena sp., Prosthecochloris sp., and microeukaryotes could be involved in this pathogenicity or could be taking advantage of the diseased state.