Whole genome sequencing has the potential to radically improve our ability to understand and manage the exceptional biodiversity of Australian fishes. Here, I illustrate the specific utility of whole genome sequencing in Australian fish biology via a series of collaborative multi-institution projects integrating conservation, taxonomy, and evolutionary biology. I show how genome sequencing of Australian fish species can improve our ability to manage threatened biodiversity, resolve taxonomic challenges at a variety of evolutionary timescales, and facilitate the study of broad-scale evolutionary patterns across vertebrates. I also showcase how performing both sequencing and bioinformatic analyses within the country can build capacity while enhancing the influence and impact of Australia’s next generation of fish biologists.