The Department of Microbiology started in the University of Nigeria, Nsukka in 1965 as a service unit headed by Professor L.C. Ferguson, who was also the Dean of the Faculty of Science. The first indigenous academic staff of the unit was Prof. Nduka Okafor. In 1967 he was joined by Prof. A. N. U. Njoku Obi from the University of Lagos, who subsequently succeeded Prof. Ferguson as Head of the Unit. The Unit was upgraded to a full department in 1970 with a core staff of seven individuals made up of five academic and two technical staff.

The Department admitted 18 pioneer students for both single and combined honours programmes. These pioneer students graduated in 1973. However, the Department graduated one student ahead of the pioneer set in 1972. This student had transferred to the University of Nigeria from the University of Ibadan following the civil war and was placed in the second year, ahead of the pioneer students.

In addition to its single and combined honours degree programmes, the Department established a Medical Laboratory unit at the Faculty of Medicine, Enugu Campus and employed a staff of the Department to teach microbiology to medical students. The unit at Enugu remained under the administration of the Department at Nsukka until 1984 when it became an autonomous Department of Medical Microbiology in the Faculty of Medicine, Enugu campus.

The Department of Microbiology today offers courses leading to B.Sc. (Honours) degree in Microbiology, Postgraduate diploma in Brewing Science and Technology, M.Sc in Medical Microbiology, Environmental Microbiology, Food/Industrial Microbiology and Brewing Science and Technology and Ph.D. in Medical Microbiology, Environmental Microbiology and Food/Industrial Microbiology. Admission into first degree programme is either by entrance Examination (UME) or by Direct-Entry. Undergraduate students admitted by entrance examination undergo a four-year programme while those admitted by direct entry do a three-year degree programme.