The chapter highlights the vital role of genetic markers in improving aquaculture sustainability and production. Genetic markers, recognizable DNA sequences associated with significant traits, are crucial for enhancing growth rates, disease resistance, and stress tolerance. Initially dependent on protein-based markers, breakthroughs in DNA-based technology, including SNPs and high-throughput sequencing, have transformed genetic analysis. These techniques tackle the intricacies of aquaculture species, which display varied genetic and biological traits. Genetic markers facilitate selective breeding, conservation genetics, and population management by identifying quantitative trait loci (QTLs) and maintaining genetic diversity. The chapter defines approaches, including species selection and marker validation, emphasizing their utilization in selective breeding, disease resistance, and sex determination. Despite challenges such as high costs and ethical concerns, genetic marker development remains integral to advancing aquaculture’s sustainability and productivity. Despite challenges such as high costs and ethical concerns, genetic marker development remains integral to advancing aquaculture’s sustainability and productivity.