The Department maintains a modern laboratory facility and state-of-the-art equipment to ensure quality instruction and research, in support of the university’s mission-vision. It has lecture and laboratory rooms for both undergraduate and graduate programs, stockroom staffed by two lab technicians and specialized room for algal culture as well as a mini-library at the Marine Biology Section. Some instruments used mainly for research and special experiments are housed in the Instrumentation Room (in-charge: Mr. Antonio Tambuli). With its number of microtomes, the Department also makes its own specimen slides used in routine laboratory exercises and for research. Aside from the laboratory facilities in the Arnoldus Science complex, graduate students are also provided with more space at the 4th floor of the AS Building.

The Department boasts of a Biological Museum (located at the 4th floor of the AS building) that serves as a repository of more than 50,000 indigenous flora and faunal specimens collected from all over the Philippines. The faunal collection is mostly insects and marine fish and corals. The floral collection (now at ca. 16,500 specimens) consists of woody plants, ferns, mosses, marine algae and marine angiosperms, and is especially stored in the Herbarium Room. Plant pathology and physiological research can also be conducted in the Greenhouse located in front at the eastern wing of the Arnoldus Science Building.

The Marine Research Station in Maribago, Mactan Island, serves as a field facility to conduct research on live marine organisms readily found in the littoral seawaters. The station has modest facility for the conduct of research in aquaculture, eco-physiology and oceanography. A 50-ft research vessel named M/B Heinrich Schoenig supports sea-based researches. The Marine Station was the site of a UNESCO Marine Biology Training Program in 1976, with participants from 7 Asian countries, as well as other training workshops.