Genetic diversity forms the basis for all other levels of biodiversity, and conservation and management efforts are increasingly incorporating genetic information into their assessments and planning. The production of reference genomes, therefore, is increasingly essential to facilitate research into biodiversity, evolution, conservation, aquaculture, and biosecurity, including pest and disease management. However, genome assembly for Australian fish lags, with a recent audit revealing only 26% of freshwater species and just 3% of marine species are represented in genomic databases. To address these gaps, the Australian Fish Genomics Initiative (AFGI) is driving reference genome assembly for over 80 species of Australian fish. The Australian Tree of Life project, hosted by the Australian BioCommons, is producing a Genome Engine to automate assembly of reference genome data collected by AFGI, as well as other framework projects. We are also exploring opportunities to develop applied tools for genomic resources in collaboration with the communities who use them. This initiative promises to accelerate the development of genomics infrastructure in Australia, enable genomics approaches in fish and fisheries science, and remove barriers to reference genome production for Australian species.