Disease outbreaks are implicated in coral reef degradation worldwide, but currently little is known about the role of viruses in coral health. In this study, transmission electron microscopy (TEM) was employed in parallel with flow cytometry to compare viral communities associated with visually healthy and white syndrome (WS)-infected tissues of the coral Acropora hyacinthus at Lizard Island on Australia’s northern Great Barrier Reef. Viral community shifts were observed on WS-infected corals that were characterized by higher abundance, smaller size and distinct morphology of virus-like particles (VLPs) on disease lesions relative to healthy tissues. Coral tissues displaying WS disease signs contained 65% more VLPs with 87% of these falling in the sub-100 nm size range, compared to only 7% from healthy tissues. While the observed viral community shifts are not necessarily indicative of disease causation, they may provide diagnostic criteria to discriminate between distinct, but macroscopically similar WS and WS-like coral diseases. Furthermore, these results highlight the need to incorporate virology in future investigations of coral health and disease.