Low-cost sequencing and -omics technologies can provide key insights into the community structure and function of microbial populations in aquaponics systems. This technology has been widely utilized to characterize the microbiome of agricultural and ecological systems. Despite the essential role of bacteria in aquaponic systems, investigation into the taxonomic structure and function of microorganisms has been limited. This presentation will highlight the different mechanisms by which genomic research can improve our understanding of how aquaponics system function. Specific emphasis on genomic techniques and pipelines will be covered, as well as broader applications of this technology to improve nutrient cycling, plant-driven rhizosphere development, nitrification, and food safety. Current and future aquaponics microbiome research at Kentucky State University will be discussed. Using a combination of both real-world and lab-scale objectives, we will compare the taxonomic profile of aquaponics systems across the United States and evaluate how environmental parameters influence the composition of microorganisms responsible for phosphorous cycling.