As technology and engineering allow mankind to survey nature at finer scales, the importance of bacteria has been elucidated in their metabolic diversity, ability to transfer genetic information, involvement in biogeochemical cycling, and sheer abundance. With an individual domain of life unto themselves, this diverse group of microorganisms plays an integral role in facilitating life on land and in the oceans, and is second only to viruses in abundance on Earth. They carve niches in a wide range of environments, including those inhospitable to other life forms, and reside in concert or to the detriment of other microbes and/or hosts they inhabit. Solely culturing microorganisms has proven to severely underestimate microbial numbers, capturing less than 1% of marine microbes. However, the advent of molecular methods has revealed the ubiquity, abundance, and diversity of bacteria. Higher organisms have evolved varying degrees of ecological relationships with bacteria, ranging from mutualism to parasitism. As the microbial players are elucidated, determining the specificity and functional roles of these bacteria is a critical and exciting scientific question. The microbiome of corals is an interesting model of complexity, with the animal host striving to maintain a delicate symbiosis, and using its microbiota to assist in nutrient cycling and protection. A contrasting example to the well-studied cnidarians are ctenophores, gelatinous organisms that are globally distributed in the world's oceans, yet the literature contains few studies on microbiota associated with this unique group of animals. Since ctenophores are one of the earliest diverging, extant multicellular animals, these unique organisms could prove to be a better model system than cnidarians. The first project in this dissertation examined spatial structure of bacteria across wild, healthy colonies of the coral Montastraea annularis. Microscale heterogeneity of the bacterial community was observed in coral mucus samples collected tens of centimeters apart on the same coral colony, which has implications for sampling strategies in microbiological studies, and impacts the application of the bacterial community as a proxy for determining coral condition in coral restoration projects. The second project looked at the linkages between coral bacterial community composition and zooxanthellae clade in Pocillopora damicornis, and results suggested that clade is not a major factor in influencing coral bacterial community composition. Sample location was also considered in the P. damicornis bacterial surveys and determined to be driving community structure. The third project is the first study to describe bacteria associated with ctenophores (Mnemiopsis leidyi and Beroe ovata). The ctenophores contained bacterial communities that were distinct from the surrounding water column, and temporal variability was exhibited by bacteria associated with the ctenophores. Exploring microbial landscapes in cnidarians and ctenophores to understand microbial roles in health and disease is the uniting theme of the three separate projects that will be discussed in this dissertation.