- Corals have multiple roles in maintaining ocean health and are some of the world’s most diverse ecosystems. The coral animal is host to a multitude of taxa, including symbiotic dinoflagellate algae, fungi, bacteria, protists, and viruses. Environmental stressors and disease agents can perturb the delicate balance of the coral host and its microbiota, which can lead to disease. This ultimately results in reduced fitness and/or mortality. There are over 30 described coral disease signs, but with a few exceptions, little is known about their potential etiological agents. Without knowledge on the causes of these diseases, little can be done to mitigate future outbreaks. Chapter 1 of this dissertation provides examples for studying novel diseases in difficult to study organisms with the use of metagenomic tools. Armed with these metagenomic tools and electron microscopy, this dissertation aimed to determine potential pathogens in two coral diseases, White Plague disease (WP), and Growth Anomalies (GAs). First, I set to determine whether viruses may be involved in WP disease from a 2010 outbreak in the US Virgin Islands (USVI). In chapter 2, I compared viromes from 21 Montastraea annularis samples (7= Diseased, 7= Diseased=Bleached, 5= Bleached, 2= Healthy) and surrounding seawater (n=2). After comparing the viromes, I found that small circular REP- encoding eukaryotic ssDNA viruses (SCSDv) similar to circo and nano viruses were associated with WP diseased tissue, and thus potential pathogens. Electron microscopy confirmed the presence of viral particles, and absence of bacterial infection in WP diseased tissue. Even though it was likely that viruses are involved with WP it was still important to understand the changes in bacterial community and the roles of bacteriophages during WP coral infection to characterize opportunistic microbes. These questions were addressed in Chapter 3 where I described the bacterial communities and bacteriophage consortia associated with the USVI corals. I also constructed phage-bacteria networks to understand which phages may interact with bacteria of interest (those shown to be differentially abundant in Montastraea annularis of different health states). I determined that there was a range of interaction specificity across the different phages and bacteria. Chapter 4 aimed to elucidate a potential pathogen responsible for Growth Anomalies, a chronic disease resulting in skeletal deformities, loss of symbiotic algae and reduction of fitness in Hawaiin Porites lobata. By comparing microbial and viral metagenomes across health states I was able to determine any changes in composition from healthy and diseased corals. Overall, microbial communities and viral consortia did not vary across health states. The hypothesized Porites spp. symbiont Oceanspirillales was dominant in all libraries. However, relative abundances of taxa in the orders Vibrionales and Verrucomicrobiales were elevated in diseased compared to healthy corals and healthy appearing tissue of GA infected corals. In addition, bacterial functional pathways remained stable across health states, while signatures of virulence factors were elevated in diseased viromes from healthy. Lastly, chapter 5 summarized overall trends of microbes and viruses determined through the studies. In addition, suggestions for future studies were outlined. Overall, this dissertation revealed a potential viral pathogenic group for white plague disease, explored how phages can influence bacterial opportunists in corals of different health states, and determined bacterial orders and virulence factors that are associated with Growth Anomalies. This dissertation includes the first study to find an association between a viral group and coral disease. In addition, this dissertation contains the first (to date) phage-bacterial inferred network constructed from paired phage-bacteria metagenomes.