Department of Botany was founded and headed by the late Professor Ali M. Eunus in 1963. The department started functioning academically with the admission of 10 students to M.Sc. Final year, who passed B.Sc. (Hons) examination from Rajshahi College. M.Sc. Previous class was started in 1964 and B.Sc. (Hons) in 1965. The department was originally housed in the Zuberi Guest House and subsequently in the First Science Building, Second Science Building and finally in the Third Science Building.
After the independence and subsequent promulgation of the Rajshahi University act (1973), Professor A.M. Eunus was appointed as the first Chairman of the Department. Afterward, Professor Asheque Ahmed,
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