The gut microbiome comprises a number of abundant and diverse organisms which play an important role in the host systems overall health. A change in factors, such as diet, age, cultivation condition and disease can influence and shift the gut microbiome from a healthy to dysbiosis state, resulting in poor growth, weight loss, susceptibility to infection, and in severe cases, mortality. While the gut microbiome of humans and various animal models has been studied extensively, knowledge on the gut microbiome of teleost fish species is in its infancy. Here, we characterized the gut microbiome of yellowtail kingfish (YTK), an important aquaculture potential species currently farmed in Australian waters, under two settings. The first being variant culture conditions (land vs sea-cage culture) and the second being different health status classifications (health vs intermediate vs unhealthy). Wild YTK and environmental water samples were also collected as critical reference points. Using next generation sequencing of the V1-V2 region of the 16S rRNA gene, we observed a change in the gut microbiome across both settings highlighting a shift to an alternate state dependent on cultivation conditions and healthy status. The key bacterium as drivers of this shift were classified using sequence databases and information was gained on their pathogenicity through literature searches. Opportunistic pathogens, which were also zoonotic, were identified, which provides valuable information to the YTK aquaculture industry in terms of both favorable and unfavorable culture and health conditions.