The yellowtail kingfish (Seriola lalandi), a carnivorous species native to tropical and temperate waters of the Southern Hemisphere's Pacific and Atlantic oceans, is in high demand, driving its commercial aquaculture in countries such as Australia, the Netherlands, Germany, the USA, Denmark, and Chile. With wild fisheries depleted, aquaculture and breeding programs are vital for enhancing profitability. While Genomic Selection (GS) is well-established in salmonids, its application in marine species like S. lalandi has been limited by scarce genomic resources and challenges from natural mass spawnings, which cause genetic bottlenecks due to asymmetric parental contributions. This study implemented GS to improve harvest weight in S. lalandi farmed in recirculating aquaculture systems (RAS) in northern Chile. We developed previously a reference genome, genotyping array, and low-density genotyping-by-sequencing (GBS) panel, to assess GS strategies. Results demonstrate that a low-density GBS panel enables cost-effective GS, maintaining costs comparable to conventional paternity-based breeding programs while improving breeding value prediction accuracy by up to 20 % to 25 %. These findings offer a practical framework for designing efficient, cost-effective breeding programs for S. lalandi in RAS, addressing its biological constraints and advancing GS in marine aquaculture for a sustainable use of this resource.