Aquaculture is the fastest-growing sector in global food production, playing a pivotal role in addressing food security challenges amid population growth, climate change, and resource limitations. However, with the growing demand for fish protein, it is necessary to implement sustainable aquaculture practices to decrease the dependence on wild fish stocks. Comparative genomics now offers a powerful technology for identifying the relationships between specific genes and various traits, including growth rate, disease resistance, heat and cold tolerance, and reproductive efficiency. Technological advancements, including next-generation sequencing (NGS) and genome editing tools such as CRISPR/Cas9, have revolutionized selective breeding, enabling precise genetic modifications to enhance productivity. At the same time, the integration of artificial intelligence (AI) and bioinformatics accelerates genome-wide association studies (GWAS). This enables the identification of beneficial genomic variants in a novel and somewhat surprising manner. However, challenges such as genomic data complexity, ethical concerns, and species-specific genomic gaps remain. Different Genomic technologies offer a powerful tool that can be used by researchers and stakeholders alike to optimize the genetic and breeding traits, thus leading to long-term sustainability and the expansion of globally productive aquaculture.