The Department of Biology starts with B1 and B2 courses in Natural and Natural Sciences organized by the Faculty of Natural and Natural Sciences (FIPA) of Gadjah Mada University (UGM). On August 1, 1960 the Department of Biological Education opened at the Faculty of Pedagogy UGM, which on January 1, 1962 entered the FKIP-B UGM. Starting May 21, 1964 the status of the UGM FKIP-B changed to FKIE IKIP Yogyakarta and apart from UGM and subsequently became the Faculty of Mathematics and Natural Sciences (FMIPA). Meanwhile the Department of Biological Education was renamed the Department of Biological Education. The Study Program that was owned at that time was only the Biology Education Study Program which had been established since 1984.

After IKIP Yogyakarta was changed to Yogyakarta State University (UNY), with a wider mandate, based on the Decree of the Director General of Higher Education No.240 / DIKTI / Kep / 1997 a Biology Study Program was established under the Department of Biology FMIPA UNY.

Department of Biology FMIPA UNY has two study programs, namely Biology Study Program and Biology Education Study Program, and has an integrated laboratory in one 3-story building, namely: (1) Microbiology, Biotechnology and Research Labs; (2) Lab. Botany; (3) Zoology Labs; (4) Ecology, Environmental Sciences, Basic Biology, Animal House and Green House Labs; (5) Lab Workshop, Lab Tenik and TIK; and (6) Outdoor Lab. Each Laboratory is in charge of various practicum and research activities, both lecturer research and student research. The laboratory is also equipped with a library, computer and internet room, learning media workshop and room for microteaching clinics. The laboratory also has gardens and experimental ponds, Green House and Animal House which are used to support practicum, research and as a means for Income Generating.