Viruses drive the evolution of animal life through direct manipulation of host biology. The objective of this dissertation was to understand how the viruses associated with reef-building corals interact with host cellular processes in order to provide insight into the evolution of Metazoans. One mechanism viruses use to manipulate their host involves the expression of viral homologs to host immune proteins. To determine whether viral populations could be used to predict immune system structure a bioinformatic approach was utilized. Viral sequences were compared to the host proteome using BLASTx revealing viral homologs to host proteins involved with cell cycle control, transcription, and immunity. Viruses can also impact the evolution of host genomes through the donation of genetic material. Here I provide evidence of an ancient endogenous retroviral infection of the protocnidarian ancestor. This novel ERV family is associated with Fibroblast Growth Factor Receptors (FGFRs) in all three cnidarians investigated suggesting that it is involved with cnidarian-specific developmental traits. Viruses affect host immunity and genome structure however hosts can resist viral invasion through programmed cell death or apoptosis. The Tumor Necrosis Factor Receptor ligand Superfamily (TNFRSF) is a central mediator of apoptosis in vertebrates, though previously uncharacterized in cnidarians. Bioinformatic analysis revealed that corals possess more TNFR's than any organism described thus far, including humans. Furthermore, corals harbor all of the central components of the canonical death receptor pathway. Empirical studies demonstrated that Human TNF_ could bind to coral cells, induce apoptotic blebbing, and cause coral bleaching. The reciprocal experiment where human cells were exposed to a coral TNF also resulted in apoptosis. These results demonstrate remarkable conservation of the TNF-apoptotic response that has been functionally maintained for over 550 million years. In summation this dissertation work provides novel insight into cnidarian biology with broad application to the origin of metazoan diversity.