The Australian Fish Genomics Initiative (AFGI) was launched by Bioplatforms Australia and Minderoo Foundation in 2024 to generate reference genomic data for Australian fishes, accelerate the development of genomics infrastructure in Australia, and enable genomics approaches in fish and fisheries science. Here, we showcase some results of the Initiative, and highlight some of the research projects in which the data have been used. Partnering with 36 project leads across 22 institutions, AFGI has so far delivered sequencing data for the assembly of 54 de novo genomes across 49 species, as well as whole genome resequencing data for eight species, with further sequencing still in progress. These data have facilitated broad-scale studies of adaptation and speciation mechanisms in Australian fishes, as well as studies of intraspecific genetic diversity and population connectivity in both threatened species and commercially important fisheries species. AFGI data have also been used to develop, test, and publish bioinformatics workflows for genome assembly and population genetics analyses, improving capacity for Australian researchers to utilise genomic data in future fish and fisheries science. Together, these outcomes build national bioinformatics capability and provide foundational resources for the research, conservation and sustainable management of Australia's unique fish biodiversity.