Previous studies of coral viruses have employed either microscopy or metagenomics, but few have attempted to comprehensively link the presence of a virus-like particle (VLP) to a genomic sequence. We conducted transmission electron microscopy imaging and virome analysis in tandem to characterize the most conspicuous viral types found within the dominant Pacific reef-building coral genus Acropora. Three of the dominant VLPs identified were observed in all tissue layers and budding out from the epidermis, including viruses that were ~70 nm, ~120 nm, and ~165 nm in diameter these VLPs all contained electron dense cores. These morphological traits are reminiscent of retroviruses, herpesviruses, and nucleocytoplasmic large DNA viruses (NCLDVs), respectively. Some 300-500 nm Megavirus-like VLPs also were observed within and associated with dinoflagellate algal endosymbiont (Symbiodinium) cells. Abundant sequence similarities to a gammaretrovirus, herpesviruses, and members of the NCLDVs corroborated these morphology-based identifications. Additionally sequence similarities to two diagnostic genes, a MutS and a DNA polymerase B gene, were recovered and most closely resembled Pyramimonas orientalis virus, demonstrating the association of a cosmopolitan Megavirus with Symbiodinium. We also identified several other viral particles in host tissues, along with sequences phylogenetically similar to circoviruses, phages, and filamentous viruses. Given that all corals in this study had high titers of viral particles and that aerial exposure of coral colonies during extreme low tides induced bleaching on the reef flat in the weeks during this work, we hypothesize that our collections and experiment coincided with a natural outbreak of viral infection.