For many countries, the COVID-19 pandemic highlighted their reliance on other nations for food security. Singapore responded with a government initiative to produce 30% of the country’s nutritional needs by 2030, and emphasising aquaculture production. One of the fish of interest is tropical red snapper (Lutjanus spp.), but there are currently issues related to seedstock quality and lack of genetically improved strains. While a popular and valuable market fish (US$13/kg), little is known about Red Snapper regarding instigation of a selective breeding program, including what species is farmed in Singapore. To resolve this and build the genomic resources and quantitative parameters useful for an advanced breeding program, a project is underway to establish: species identity, a genome, a population based genetic audit, a 70K SNP array, coupled with heritability and quantitative genetic parameter estimates. DNA barcoding identified the Malabar Red Snapper (L. malabaricus) as Singapore’s principal market species. A Singaporean sourced snapper was then used to produce the first genome of Malabar Red Snapper with an estimated genome size of 1Gb, with 24 chromosomal level scaffolds comprising 98.6% of the genome, n50 of 42,082,220 bp, and BUSCO score of 98%. This assembly was used to call SNPs for downstream genotyping-by-sequencing analyses. A population genetics study of ~1,000 fish from throughout the Indo-Pacific further unravelled the population structure and dynamics of Malabar Red Snapper. Setting this early foundation of genetic resources will help streamline establishing a new selective breeding program and optimize our capabilities for genetic prediction for improved commercial traits.