Genomic tools have transformed fish breeding programs, enhancing the precision and efficiency of selecting desirable traits in aquaculture. This chapter explores the role of these tools, including genome sequencing, genotyping, and GWAS, in improving growth rate, disease resistance, and reproductive performance of fish. It also discusses functional genomics, epigenomics, and gene editing technologies like CRISPR-Cas9, which are crucial for understanding and manipulating fish traits. Despite challenges like high costs and limited data, advancements in bioinformatics and sequencing are paving the way for more sustainable and productive aquaculture practices.