The history of the Department of Botany dates back to 1912, when the study of Natural Science was introduced at the Intermediate courses. Rev. Fr. Gombert, SJ, was guiding the Botany and Zoology sections. The Students of the Natural Science stream occupied the top slots in the medical and engineering centers of the country. The Botany course was introduced in 1930 as an ancillary subject to the B.Sc., and B.A., major courses. From 1952 onwards Rev. Fr. Rapinat pioneered the department. Under his guidance the B.Sc., degree Botany course was started in 1952. He made extensive collections of plants and preserved them in the herbarium. He equipped the laboratories and library with a view to start post-graduate course. The M.Sc., degree in Botany was introduced in 1958, and the department was the first to offer it outside the Madras city in Tamil Nadu. The department was primarily engaged in preparing the students in B.Sc., and M.Sc., degrees till 1973, when the Research section was opened by the initiative of Rev. Fr. J. L. Gnanarethinum SJ. Research activities were conducted in plant physiology, plant biochemistry, palynology and ecology.
When this college became autonomous in 1978, a thorough reorientation was given to the B.Sc., and M. Sc., courses making them socially relevant and research oriented. The Rapinat Herbarium, a center for Plant Taxonomic research has its origin from this department. A large number of herbarium specimens, books, reprints and journals have been gifted to the herbarium and this formed the nucleus around which it expanded to the present status of international repute. Reading the signs of times and demand generated for job oriented modern programs the department of Botany took the initiative to offer M.Sc., Biochemistry as an interdisciplinary course in 1992. Later in 2001, M.Sc., Biotechnology course was started. Projects funded by UGC, DST, CSIR, DBT, MoEF and NMPB have been sanctioned.
The department is provided with a mushroom culture centre in which students of UG are trained in mushroom cultivation and also in its marketing strategies. The department has five research centres such as tissue culture, microscopic, cryptogamic botany, mushroom cultivation and microbial culture collections. The department has obtained Grant from DST and FIST Programme in the year 2010. Till now 62 scholars have obtained Ph.D degree and 195 got their M. Phil degree. The department has signed MoU with renowned organizations such as KS Varier`s Ashtanga Ayurvedic (P) Ltd., Tiruchirappalli, National Research Centre for Banana, Tiruchirappalli, ANSA Herbs and Food (P) Ltd, Tiruchirappalli and Indian Institute of Crops Processing Technology, Thanjavur. The department established a Solid waste recycling plant in the Academic year 2017-18 where the solid waste of the campus is processed and converted into vermicompost which is supplied to farmers in concessional rate.