Research on coral microbial communities—the coral microbiome—has often focused on the pathology of coral diseases, many of which are thought to be caused by bacteria. Without understanding the structure and variation of healthy coral microbial communities, however, we cannot fully understand how changes in the coral microbiome produce disease. To address this problem, we characterized healthy coral microbiomes of 100 coral colonies from six Caribbean coral species across four reef sites and three time points over one year.