Global change increasingly requires intensive management of fisheries resources and wild fish populations. We stock fish to support fisheries, translocate individuals to re-establish or connect populations, and use captive breeding and genetic rescue to restore diversity for threatened species. These interventions depend on baseline knowledge of the genetic diversity, inbreeding and relatedness of the populations involved. They also depend on the capacity to record, persist and update information as long-term projects evolve. FishGen is a collaborative project for sustained genomic monitoring that provides a framework for management of iconic fishes in the Murray–Darling Basin. FishGen links genomic sequences with sample metadata for thousands of hatchery broodstock and wild fish in a single centralised database. It facilitates ongoing monitoring of diversity, inbreeding and kinship, identifies stocked fish in the wild, and tracks their movement. Genetically informed breeding guidance is provided to hatcheries via individual tailored reports and a cloud-based data portal. As new samples are added, the framework both describes current genetic health and detects change as it emerges. The same architecture of centralised data, genomic baselines, parentage-based tagging and breeding management tools can be applied in freshwater, estuarine and marine systems alike, and for both fisheries and conservation. FishGen lays the foundation and provides a conceptual model for sustainable long-term monitoring and evidence-based management of many species under a changing climate.