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 generate large genetic datasets for estimating abundance, population structure and connectivity. The success of these studies, however, relies heavily on efficient field and laboratory methodologies. Application of these methods for high throughput population genetics would not be cost-effective without a streamlined procedure that incorporates specialised processing of tissue samples and database management. Integrating novel sampling tools and streamlined laboratory protocols, we have developed specialised high throughput tissue collection and analysis methods that permit up to 2,000 DNA extractions per day. Our approach has been successfully applied to southern bluefin tuna (Thunnus maccoyii) and has delivered fishery independent data on absolute abundance of juveniles (Gene Tagging program) and a census of adult spawning numbers as key parameters for Close Kin Mark Recapture (CKMR), that have transformed the international monitoring and management of this iconic fishery. This initiative has been instrumental in the Australian Southern Bluefin Tuna Purse Seine Fishery obtaining certification as sustainable under the Marine Stewardship Council standard, and delisting of this species from the EPBC threatened species list. Our work has now been extended across global fisheries and oceans, with our current focus on tuna species in the Pacific Ocean. Our goal is to enhance and standardize these high-throughput genetic protocols so that they can be utilized across various fisheries, thereby improving the availability of high-quality data streams for effective fisheries and conservation management.