Oyster cultivation contributes to a significant portion of Australia’s aquaculture production, which is valued at approximately $100 million per annum. Production has recently been impacted by disease outbreaks that have decimated oyster farms, ultimately reducing the supply of commercially available oysters. Pacific oysters (Crassostrea gigas) are a key commercial species both locally and globally, however, during the last two decades, a disease known as ‘summer mortality’ has heavily impacted the cultivation of Pacific oysters around the world. The exact causes of summer mortality are poorly understood, however, a few microbial agents have been implicated in this disease, including ostreid herpesvirus (OsHV-1) and bacteria, particularly from the genus Vibrio. Emerging evidence suggests that these mortality events are a multi-factorial problem caused by converging environmental and biological factors. One important biological factor is the microbial community (microbiome) that colonises the oyster. Recent studies have indicated that the oyster microbiome can be shifted as a consequence of changing environmental factors, particularly temperature stress, which can also impact the susceptibility of the oyster to infectious diseases. Currently we have a limited understanding of the Pacific oyster microbiome and the role it plays in disease events. To explore this further, we examined the microbiome of Pacific oysters during a summer mortality event in Port Stephens (NSW) in 2013-2014. By combining molecular approaches with network analysis, we have begun to identify links between the oyster microbiome, changing environmental conditions and oyster disease events.