Coral reef communities of the Seychelles have been subjected to repeat El-Niño driven heat waves over the past 35 years, driving periodic mass coral bleaching. Coral associated microbes (i.e., Symbiodinium and bacterial communities) influence how coral bleaching manifests but remain undescribed for Seychelles’ reefs. We therefore examined microbiome diversity and composition at the peak of the 2016 heat wave in the Seychelles for key coral taxa considered bleaching sensitive (Acropora muricata, Acropora gemmifera) versus tolerant (Porites lutea, Coelastrea aspera), and at two contrasting reef sites (clear water versus turbid).