As the world’s largest producer of certified sustainable palm oil, Sime Darby has an utmost focus in realizing the potential of its oil palm materials; enhanced genetic gain for quantitative traits such as oil extraction rate (OER) and fresh fruit bunch (FFB) at low production cost. With the impending needs to increase the mean performance in commercial planting followed by the robust in-house genomic research; Sime Darby Plantation has decided to embark on implementation of marker-assisted selection (MAS) in our commercial seed production. We have developed and optimized a deployment pipeline tailored especially for oil palm from the available high throughput technology in the market. Sampling of 40,000 leaf tissues per month, extraction capacity that stands up to 30,000 samples per month and genotyping platform that can process 5 million data points per month are the key components that enable commercial-scale seed production in Sime Darby Plantation. In order to facilitate handling of a very large amount of data, we have built bioinformatics tools and pipelines that are able to efficiently bring information for MAS of elite oil palms. Despite many challenges, high throughput marker deployment in oil palm is now made possible and will provide an unprecedented opportunity for the next oil palm improvement programs.