The Department was founded January 1, 2013, when the former Department of Botany and Department of Systems Ecology were merged and named the Department of Ecology, Environment and Plant Sciences.

Botany was established in 1882 as an autonomous department with its own professorship at Stockholm University, which at that time was called Stockholms högskola. Eugen Warming held the professorship and became Stockholms högskola’s first elected Vice Chancellor. Department of Botany later moved to premises specially built for the purpose in Lilla Frescati with inauguration in 1964.

The Department of Systems Ecology originated in the Askö Laboratory, founded in 1961 by Professor Lars Silén. At the end of the 70s resources were moved to Stockholm University to continue the marine ecosystem research with a professorship in marine ecology. 1989 Department of Systems Ecology was formed, with professorships in Marine Ecology, Marine Ecotoxicology, Brackish Water Ecology, and Natural Resource Management.

In 2013 the Department of Ecology, Environment and Plant Sciences was formed by merger of the two departments. A couple of years later, during the summer 2015, the department moved together in newly built premises in the Arrhenius laboratories. The department currently conducts a broad research and teaching with professorships in the research topics Ecotoxicology, Marine Ecology, Plant Ecology, Plant Physiology and Plant Systematics.