Lynn Margulis was a faculty member in the Biology Department at Boston University before she took her present position as Distinguished University Professor at University of Massachusetts-Amherst. She taught and researched in the Boston area, including at the Boston University Marine Program, Woods Hole MA for over 22 years. She has been a member of the United States National Academy of Sciences since 1984 and in 1999 received a National Medal of Science from President William Clinton.

A keen admirer of Charles Darwin, she and her advanced students are profoundly grateful for recognition by the Linnean Society of London (2008 Charles Darwin- Alfred Russel Wallace silver medal for "major advances in evolutionary biology since 1958"). She suggests that the research and teaching successes of her current and former advanced students are based on their grasp of "environmental evolution". Based on scientific collaboration with geologists and other environmentalists including especially James E. Lovelock, FRS, father of the Gaia hypothesis, she developed and has taught the "Environmental Evolution: Effect of Life on Planet Earth" course every year since 1972.

Professor Margulis, since 1988 a faculty member in the Department of Geosciences in Amherst, is an "evolutionist", not an evolutionary biologist. Life's evolutionary story, she posits, requires understanding of environmental context: Earth. Evolutionists love nature; Darwin's field in recognition of his excellent grasp of geological processes, she thinks, should still be called "Natural History". Reconstruction of the history of life encompasses (besides botany, systematics, microbial ecology, genetics, proteomics and most other biology) at least: astronomy, comparative planetology, field geology (e.g., geochronology, paleontology, sedimentology) and chemistry (atmospheric, metabolic and bio-).

In her research and teaching with many collaborators, primarily students, she details the multiple symbiotic origins of nucleated cells from bacterial antecedents. This concept is best known as the Serial Endosymbiosis Theory or SET (named by protistologist Professor F.J.R. Taylor, University of British Columbia, Canada). Presented as Origin of Mitosing Cells, (1966) she developed the idea of Symbiosis in Cell Evolution: Microbial communities in the Archean and Proterozoic eons, 3rd ed., in her book-length monograph. Unbeknownst to English, French or German literature symbiogenesis as major source of hereditary novelty integrated with Chas. Darwin's prodigious concept of "descent with modification" shaped by "natural selection" was expounded in Russian by botanist B. M. Kozo-Polyansky from Voronezh, "Black Earth Russia" author of Symbiogenesis, a New Principle of Evolution, 1924). Despite opposition mainly from prestigious and powerful anglophone zoologists, she continues to pioneer the recognition of symbiogenesis in the origin of eukaryotic species and their more inclusive taxa. Co-written with Michael J. Chapman she has authored Kingdoms & Domains, An illustrated guide to the phyla of life on Earth (Academic Press-Elsevier, 2009). She advocates "power to the Protoctista kingdom" whose members include some 250,000 estimated species of extant nucleated organisms. Protoctist ancestors have an underappreciated fossil record that extends from the Proterozoic eon until the Holocene. She is a co-founder of two international societies: Evolutionary Protistology (ISEP) and the International Symbiosis Society (ISS). With her students and colleagues in the field and laboratory she investigates microbial symbioses, especially bacteria and protoctists under microoxic conditions. Ecological field work on these themes has taken her beyond the northeast region of North America primarily to Mexico, Spain and Morocco.