Evidence suggests that coral-associated bacteria can be manipulated to promote specific functions and enhance coral survival during periods of thermal stress. The functions of coral-associated bacterial communities are defined by biochemically active microbes, but nucleic acid-based analytical methods, in particular 16S rRNA gene amplicon sequencing or metabarcoding, provide no information on the metabolic activities or physiological states of bacteria. Even the most fundamental physiological state, viability, cannot be assessed with DNA-targeted methods such as PCR. Combining high-throughput sequencing with a propidium monoazide (PMA) treatment that depletes signals of non-viable microbes and extracellular DNA enables the exclusive characterization of the viable community. By applying PMA to coral tissue, this project assessed the viability of host-associated bacteria in six Great Barrier Reef coral species: Acropora loripes, A. tenuis, A. millepora, Porites lutea, Platygyra daedalea, and Pocillopora acuta. Five replicate samples from five genotypes of each coral species were split in half; one fraction received the PMA reagent, while the other was left untreated as a control. All samples are currently being sequenced on an Illumina MiSeq (2x300 bp) at the Walter and Eliza Hall Institute. Results from this study will indicate which bacteria are consistently associated with each coral species and are thus likely to be symbiotic members of the microbiome. This innovative project is highly relevant to all microbiome studies and will set a standard for interpreting microbial community structure data by delivering a solution to identifying the bacteria that are active in a complex community.