The Herbarium was founded by the Jesuit priest and taxonomist, Ethelbert Blatter, SJ. It was renamed in his honour in 1941 by his associate and director of the Herbarium, Father Henry Santapau, SJ. Father Santapau went on to direct the Botanical Survey of India, and was recognized by the Indian Government with a Padmashri in 1964 for his services to Indian botany.
The two priests are regarded as pioneers in Indian plant taxonomy, and contributed over 500 scientific articles to various journals. They also wrote a number of books, like The Flora of Aden, Arabia; Beautiful Flowers of Kashmir; The Bombay Grasses; Palms of Asia; Orchids of Bombay; Medicinal and Poisonous plants of India; Flora of Khandala; Acanthaceae of Bombay, and Trees of Bombay.
The Herbarium is currently engaged in a variety of national projects, including surveys of medicinally and economically important plants of Western Maharashtra, the flora of Ratnagiri District, ethnobiology of Goa Tribals, and the trees of Mumbai.
Many scholars make use of the institute's facilities to conduct post-graduate and doctoral studies.