On June 30, 2000, the Philippine Agriculture and Fisheries Biotechnology Program, otherwise known as the Department of Agriculture (DA) Biotech Program, was established through a memorandum of agreement between the Government of the Republic of the Philippines and the Government of the United States of America in recognition of the utmost importance of biotechnology in agricultural modernization, rural development, and environmental management in the country. 

In 2006, the DA National Biotechnology Program (2006-2016) was formulated aimed at positioning Philippine Agriculture in the biotechnology century. The ten-year program outlined the recommended activities and strategies focusing on: (1) promotion of the growth of a natural ingredients industry by creating the appropriate policy environment in a multi-agency setting; (2) promotion of integrated processing of traditional crops and fishery products; (3) utilization of biotechnology in improving traditional crops, livestock, and fisheries; and (4) improvement of monitoring of R&D with emphasis on technical monitoring and requiring tangible research outputs such as publications, patentable technologies, and user-friendly technologies ready for the extension system.

In 2013-2014, the research, development, and extension (RDE) agenda of the DA Biotech Program was reviewed to be aligned and harmonized with other roadmaps or programs being implemented and managed by the Department of Agriculture and other relevant agencies.

Over the years, the DA Biotech Program has evolved to cover not only genetic engineering, but also the whole range of biotechnology tools and applications in agriculture to take full advantage of the potential and actual benefits.