The Molecular Biology and Biotechnology Program (MBBP) was established by the University of the Philippines Board of Regents in 1987 under the College of Science, U.P. Diliman. This interdisciplinary program was created to train undergraduate and graduate students in Molecular Biology and Biotechnology to respond to the need of the Philippines for molecular biologists and biotechnologists in academe and the industry. The first faculty members of the program came from the different departments of the College of Science, namely, the Departments of Biology, Chemistry and Physics. The first “home” of the program was the Natural Sciences Research Institute or NSRI.

In 1991 the MBBP moved to Albert Hall where it would stay until 2012. In 2000, the MBBP evolved into the National Institute of Molecular Biology and Biotechnology, U.P. Diliman (NIMBB-UPD) and in 2006, the NIMBB-UPD was declared a Center of Excellence by the Commission on Higher Education (CHED).

It was also during this time that the NIMBB-UPD actively implemented several extension programs designed to increase public awareness of molecular biology and biotechnology. Activities which have been part of the extension work of the NIMBB over the years were the Biotech FAQs which was a set of seminars on Biotechnology for high school and college teachers held in 2001-2002 with the support of DA-BAR and the Philippine Society for Microbiology (PSM), the creation of the REV-UP seminars for high school and college teachers in 2002 which is now administered yearly by the NIMBB-UPD in conjunction with the Philippine Society of Molecular Biology and Biotechnology (PSBMB), and the regional biotechnology seminars held in 2009 for college teachers of biology in state colleges and universities with the help of DA-BAR and CHED. In addition, the NIMBB-UPD has held several hands-on training workshops over the years to familiarize teachers from different colleges all over the Philippines with the basic techniques used in molecular biology and biotechnology.

On December 8, 2006, President Gloria Macapagal Arroyo created the National Science Complex with Executive Order 583. This enabled the NIMBB-UPD, along with the other constituent units of the College of Science, U.P. Diliman, to build its new home in the south sector of U.P. Diliman. The building was finished in October of 2012 and operations of the NIMBB-UPD at the new building began during the second semester of AY 2012 – 2013. The new building is equipped with a large central research laboratory which is shared by all the investigators of the NIMBB-UPD, four teaching labs for undergraduate and graduate classes, two large classrooms, two small lecture rooms and two meeting rooms for lecture classes. In addition, the NIMBB-UPD building also currently houses the newly established Philippine Genome Center and the Technology Transfer and Business Development Office of the U.P. System.