Sustainable management of fisheries plays a key role in ensuring food security, ecological stability, and socioeconomic sustainability of the world. The conventional methods of monitoring and evaluation are not always sufficient because of the inability to achieve high accuracy, time, and species-specificity. The recent development of molecular and genomic technology has revolutionized the ability to measure, monitor, and preserve aquatic biodiversity in a more precise manner than ever before. Genomics, transcriptomics, and proteomics have become the central activities in the dissection of the genetic architecture of fish populations, which has made it possible to identify adaptive traits, as well as population structures, that are important in the management of stocks. The DNA barcoding and environmental DNA (eDNA) methods have transformed the concept of species identification and biodiversity monitoring that enabling non-invasive detection of rare, cryptic, or endangered species. The application of population genetics and genomic selection can again assist in defining the management unit and informing breeding programs that will improve resilience and productivity. Having all these molecular advancements leads to the creation of ecosystem-based management that incorporates genetic information into policy frameworks that enhance conservation, traceability, and sustainability. Fisheries genomics continues to be extended with the integration of the multi-omics platform with the advanced bioinformatics and artificial intelligence that allows predictive and adaptive management strategies to respond to environmental change. All molecular and genomic technologies are a revolutionary direction of sustainable, information-driven fisheries management, which combines the preservation of the ecological environment with human nutritional requirements.