The Doctoral in Biotechnology Study Program is one of the Study Programs within the Graduate School of Universitas Gadjah Mada. The establishment of this Study Program began with the establishment of the UGM Inter-University Center (PAU) for Biotechnology, which is a development project in the Indonesian Biotechnology sector under the Director General of Higher Education. PAU for Biotechnology UGM was founded in 1985 based on the Decree of the Minister of Education and Culture of the Republic of Indonesia number: 909/D/T/1986 dated May 15, 1986, using World Bank XVII assistance funds from 1986 to 1995. PAU for Biotechnology UGM is one of three PAUs for Biotechnology in Indonesia.

Since the stipulation of the UGM Chancellor's Decree number: 25/P/SK/HKTL/2001 dated July 3, 2001, concerning Changes/Determination of Centers within Universitas Gadjah Mada to become a Research Centers, the PAU for Biotechnology UGM has changed to the Research Center for Biotechnology UGM. Based on the Decree of the Director of the Universitas Gadjah Mada Postgraduate Program Number: 01/J01.4/OT/SK/3, the Doctoral in Biotechnology Study Program was managed under the Biotechnology Study Program in 2003. The Doctoral in Biotechnology Study Program involves very varied fields of science and teaching staff from various faculties within UGM, therefore the Doctoral in Biotechnology Study Program is classified as a multidisciplinary study program and its management is under the Graduate School UGM based on Chancellor's Decree 89/P/SK/HT/2006.