Population genetics can be used in cost-effective and highly informative monitoring programs to improve sustainable fisheries management. Recent advances in next‐generation sequencing and high throughput technology have provided the ability for researchers to obtain large genetic datasets for estimating abundance, population structure and connectivity. Our ability to perform these studies, however, relies heavily on methods developed and applied in the field and in the laboratory. Without a streamlined procedure that incorporates data management, sample management, specialised processing of tissue samples and automated workflows, high throughput population genetics would not be cost-effective. We have developed specialised methods to collect and analyse tens-of thousands of tissue samples using novel sampling tools and streamlined laboratory protocols (Preece et al. 2021). We have successfully applied these methods to southern bluefin tuna (Thunnus maccoyii) and when combine with approaches such as Gene Tagging (GT) and Close Kin Mark Recapture (CKMR) (Preece et al. 2015), it has transformed the way the fishery is monitored. Our aim is to refine and standardise these high-throughput genetic protocols so they may be applied across a range of fisheries to improve the availability of high-quality data streams for fisheries and conservation management.