The Department of Botany, Mangaldai College, was established in the year 1969 for Pre-University classes by the founder head Late Surendra Nath Deka. The subject Botany was introduced in degree classes from the session 1970-1971, while the Major courses started from 1989-90. The department was supported by the Star College Scheme under DBT (Department of Biotechnology), Govt. of India from 2014-2019. The department is well-equipped with modern classrooms, laboratories and smart classrooms with smart boards for ideal academic development of the students. The Department is also enriched with a Vermicompost Unit, a Mushroom Production Unit, a Shade Net House, an Herbal Garden, etc. The department is run by seven dynamic faculty members headed by Dr. Prativa Deka, HoD, Department of Botany. Faculties are also engaged in active research. Apart from these, the Department is practicing conservation of plant diversity in the college campus.

Besides the Central Library, the Department has been maintaining a Departmental Library having more than two hundred valuable books along with few important journals.

The department has three well-equipped degree level laboratories consisting of essential laboratory instruments and apparatus for practical classes.

The department has two smart classrooms equipped with two smartboards (including digital smartboards) with seat capacities of 48 and 120.