Western Australia's coastline spans tropical, subtropical and temperate oceans, encompassing one of the world's strongest marine environmental gradients and an exceptionally distinctive fish fauna characterised by high endemism and complex biogeographic history. Yet much of this diversity remains genomically unexplored, with relatively few marine fish species represented by high-quality reference genomes. To address this gap, the Minderoo OceanOmics Centre at The University of Western Australia has established a collaborative initiative with the Western Australian Museum and the Department of Primary Industries and Regional Development to develop a comprehensive genome reference library for Australian marine vertebrates currently underrepresented in global repositories. The project integrates strategic field sampling with taxonomically verified museum collections to capture the evolutionary diversity of Western Australia's marine fish fauna. Genomes are linked to an expertly identified, permanently accessioned voucher specimen, providing a robust taxonomic foundation for biodiversity research, conservation, and environmental DNA (eDNA) applications. By prioritising threatened, endemic, commercially important, and phylogenetically underrepresented lineages, the project will substantially expand Australia's genomic resources and contribute openly accessible reference genomes to global databases. These resources will provide the foundation to investigate the origins of Western Australia's remarkable marine fish fauna. We aim to examine the role of Western Australia in the diversification and biogeography of marine fishes, identify the historical processes that generated and maintain the region's exceptional endemic fauna, and explore how the state's distinctive environmental gradients have shaped evolution and adaptive responses to environmental change. By integrating strategic sampling and whole-genome sequencing with museum collections, this project will establish a lasting resource for biodiversity monitoring while enabling new insights into the origins, evolution, and future resilience of Australia's marine fish diversity.