The ‘hologenome theory of evolution’, proposed by Rosenberg and colleagues1, suggests that reef corals, and by extrapolation other multicellular organisms, adapt to environmental stress by alterations in their resident microbial communities. Although this is an interesting idea, we strongly disagree with aspects of this theory, specifically those that arise from the omission and flawed interpretation of the coral literature (for reviews of omitted literature see Refs 2,3).