The Department of Botany, St. Stephen’s College, Pathanapuram was established in 1982, with B.Sc. Degree course under the University of Kerala. Over the years, it has grown into a full-fledged department with Postgraduate Botany course. Affiliation for M.Sc. Botany was granted in 2020 with specialization in Ethnobotany and Ethnopharmacology. This new generation course offers opportunities in identification of medicinal plants, separating their constituents and characterizing them based on traditional knowledge. The elevation of the department as a Research Centre of the University of Kerala in 2024 was a landmark in its history. Department has identified various thrust areas of research such as Phytochemistry, Microbiology, Ethnobotany, Ethnopharmacology, Phycology, Mycology, Biodiversity analysis etc. The Department has two laboratories for practical work and one research lab with several facilities and internet access. There is a well maintained museum with more than 300 specimens. The Department herbarium has about 700 sheets in its collection.

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