Microbial interactions in aquaculture industries are often thought of in a disease context. Indeed, diagnostic screening programs are applied throughout production cycles to detect commonly reported pathogens. For example, screening for Renibacterium salmoninarum in broodstock is routine for most salmon hatcheries while diagnostics for infectious salmon anemia virus (ISAV), among other viruses and bacteria, is common for pre-smolts prior to seawater entry. In shrimp, testing for Vibrio parahaemolyticus, white spot syndrome virus (WSSV), and infectious hypodermal and hematopoietic necrosis virus (IHHNV), among others are common for stock transfers and when mortalities are observed in culture systems. These examples of targeted screening programs have dramatically decreased incidences of disease outbreaks in aquaculture; however, there are limits on the practicality and capacity of these programs to cover the full scope of potentially problematic microbes affecting host species. Given the extensive diversity of microbes that can contribute to inefficiencies in production, exploratory diagnostic approaches are useful when gross pathology, abnormal behaviour, or mortality is observed and beginning to trend, yet the cause is unknown, the observations unexpected, and common pathogens have been ruled out. Further, understanding the entire composition of bacterial communities in aquaculture systems, including pathogens through to commensals, is proving to be invaluable. In this presentation, methodologies for sampling and detecting bacteria, ciliates, and dinoflagellates in aquaculture systems will be discussed using examples from fish and shrimp production. Molecular descriptions of opportunistic pathogens, off-flavor producing bacteria, novel ciliates, toxin-producing dinoflagellates, and the causative agent of purple salmon eggs, among others will be discussed. A particular focus on the amplification of conserved DNA loci from microbes will be examined in the context of improving efficiency and animal welfare in aquaculture.