Aquaculture, as one of the fastest-growing industries, faces an array of challenges ranging from poor growth, disease susceptibility and environmental stress. Functional genomics has become a transformative field in aquaculture, enabling comprehensive insights into the genetic and molecular mechanisms that underlie key traits such as growth, disease resistance, stress tolerance and reproductive efficiency. By exploring how genes function, interact and respond to environmental factors, functional genomics provides the aquaculture industry with data-driven tools to optimize production and address sustainability challenges. This overview explores core functional genomics techniques, including transcriptomics, proteomics, nutrigenomics, metabolomics, metagenomics and gene-editing technologies, which have empowered researchers to map and manipulate genes responsible for desirable traits in major aquaculture species, such as Atlantic salmon, tilapia, shrimp and shellfish. Applications of functional genomics in aquaculture have led to significant advancements on improved growth rates, enhanced feed efficiency, increased disease resilience and reproductive control are now achievable through genomics-informed breeding and management practices. However, the field also faces challenges, such as high costs, technical complexity and limited genomic resources for certain species and a lack of standardized protocol. Emerging trends in multi-omics integration and artificial intelligence promise to expand the impact of functional genomics, allowing for more precise selection and even personalized aquaculture systems. By addressing these obstacles, functional genomics holds the potential to revolutionize aquaculture, paving the way for sustainable, resilient and productive fish farming practices that support global food security and environmental goals. This chapter provides a comprehensive review of current advancements, challenges and future directions in functional genomics within the aquaculture sector.