The Department of Botany was established even before 1903.

Ethelbert Blatter SJ (15 December 1877 – 26 May 1934) was a Swedish Jesuit priest and pioneering botanist in British India. He became the Professor of Botany in 1903 of the St. Xavier's College, Bombay and also became the principal of the college later. He was also the vice-president of the Bombay Natural History Society. He published five books and over sixty papers on the flora of the Indian subcontinent. In 1932, he became the first recipient of the Johannes Bruehl Memorial Medal of the Asiatic Society of Bengal.

His first of research article was "The Fauna and Flora of Our Metallic Money," which somewhat humorously catalogued the microorganisms commonly found on various coins in India. In pursuit of his researches, Blatter travelled extensively within India. His most important contributions from this time were a series of articles written between 1904 and 1909 and titled, The Palms of British India and Ceylon, Indigenous and Introduced. As a professor of botany at St Xavier's college, he expended great energy during the next few years both travelling and building an extensive botanical collection. Consequently, St. Xavier's College had one of the best herbaria in Western India during those years. He was appointed principal of the college in 1919, retaining his professorial chair until 1924. He also became a prominent member of Bombay University Senate and played a significant role in influencing later university reforms.

His series of papers with W. S. Millard titled, Some Beautiful Indian Trees were published after 1925. These papers too resulted in a book of the same name, a classic. Other books on India from this time were the two-volume Beautiful Flowers of Kashmir (1927, 1928); The Flora of the Indus Delta (with Charles McCann and T. S. Sabnis, 1929); and The Ferns of Bombay (with J. F. D'Almeida, 1932). The following year he was elected Vice-President of BNHS.

In 1954, the first independent Government of India appointed the taxonomist Fr. Hermenegild Santapau as its Chief Botanist and Director. Santapau had a PhD in Botany from the London University, had worked at the Royal Botanical Gardens in Kew (England), was a Fellow of the Linnean Society of London, editor of the Journal of the Bombay Museum of Natural History, and a Professor of Botany. His services to reviving botany and science education in the country were recognized with the award of the Padma Shri from the Government of India. However, this "giant" was neither British nor Indian — he was a Catholic Jesuit priest from Spain. Fr. Santapau was only one of the many Jesuits who established a legacy of "Jesuit science" in India after the religious order was "restored" in 1814.

His student K M Matthew (1930-2004) became the first Indian Jesuit to acquire a PhD in botany, focusing on the alien plants of the Palni Hills. In 1963, another pupil of Santapau, Cecil Saldanha (1926-2002) was awarded his PhD for his thesis on Taxonomic Revision of the Scrophulariaceae of Western Peninsular India. Like Santapau, both the Jesuits made significant contributions to plant taxonomy: KM Mathew published the four-volume Flora of Tamil Nadu Carnatic (1981-1988) while Saldanha published Flora of the Hassan District, Karnataka (1976).

Young historians of Jesuit science must wonder why then Prime Minister of India, Indira Gandhi observed after Santapau's death in 1970 that: In Rev. Fr. Santapau's death we have lost an eminent scholar who has served education and science for over 40 years. His deep love for India urged him to become a citizen of the country. He had an excellent knowledge of, and concern for, our plant wealth and wrote intensively on it for experts and laypeople. May his memory long continue to inspire all those interested in our flora.