The Zoology department of Cotton College was started in May, 1942 by introducing the subject in I. Sc. Classes. B.Sc. Zoology was introduced as pass course in 1947 and got the affiliation from Gauhati University from 1948 onwards. B.Sc. (Hons.) Zoology was introduced in 1953. M.Sc Zoology started in 1974 with two special papers- Entomology and Fish and Fishery Biology. Later on, Ecology and Environmental Biology was introduced as a special paper in M.Sc. in the year 1993 and Cell and Molecular Biology in 2016. The department is also awarded with FIST (DST) and a computer lab was established. Now the department functions under Cotton University after the upgradation of Cotton college to Cotton University.