由於當時的生物學主流並不接受共生思想,因此她的理論很快地遭受駁斥。在多年的批評聲浪中,馬古利斯逐漸因她對推行內共生學說的堅持不懈而著名。她在1970年的著作《真核細胞的起源》(Origin of Eukaryotic Cells)當中,更進一步的描繪了有關於胞器起源的理論。到了1980年代,科學家們發現在粒線體及葉綠體兩種胞器內,藏有屬於它們自己DNA,且與藏於細胞核內的DNA並不相同。此發現使內共生學說得到了支持。到了現在,主流生物學界已經普遍接受內共生學說[10]。英國新達爾文主義生物學家理查德·道金斯曾經如此評論馬古利斯與她對內共生學說的研究:
Margulis, Lynn and Dorion Sagan, 2007, Dazzle Gradually: Reflections on the Nature of Nature, Sciencewriters Books, ISBN 978-1-933392-31-8 (《娓娓動人:關於自然本質的深思》)
Margulis, Lynn and Eduardo Punset, eds., 2007 Mind, Life and Universe: Conversations with Great Scientists of Our Time, Sciencewriters Books, ISBN 978-1-933392-61-5 (《心靈、生命及宇宙:與當代偉大科學家對話》)
Margulis, Lynn, 2007, Luminous Fish: Tales of Science and Love, Sciencewriters Books, ISBN 978-1-933392-33-2 (《發光的魚:科學與愛的故事》)
Margulis, Lynn and Dorion Sagan, 2002, Acquiring Genomes: A Theory of the Origins of Species, Perseus Books Group, ISBN 0-465-04391-7 (《獲得性基因組:關於物種起源的理論》)
Margulis, Lynn, et al., 2002, The Ice Chronicles: The Quest to Understand Global Climate Change, University of New Hampshire, ISBN 1-58465-062-1 (《歷代冰河誌:了解全球氣候變遷》)
Margulis, Lynn, 1998, Symbiotic Planet : A New Look at Evolution, Basic Books, ISBN 0-465-07271-2 (《共生行星:演化的新見解》)
Margulis, Lynn and Karlene V. Schwartz, 1997, Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth, W.H. Freeman & Company, ISBN 0-613-92338-3 (《五大生物界:地球生命各大門圖說》)
Margulis, Lynn and Dorian Sagan, 1997, What Is Sex?, Simon and Shuster, ISBN 0-684-82691-7 (《性是什麼?》)
Margulis, Lynn and Dorion Sagan, 1997, Slanted Truths: Essays on Gaia, Symbiosis, and Evolution, Copernicus Books, ISBN 0-387-94927-5 (《傾斜的真相:論蓋亞、共生與演化》)
Margulis, Lynn, 1992, Symbiosis in Cell Evolution: Microbial Communities in the Archean and Proterozoic Eons, W.H. Freeman, ISBN 0-7167-7028-8 (《細胞演化中的共生:太古時期及古代的微生物共同體》)
Margulis, Lynn, ed, 1991, Symbiosis as a Source of Evolutionary Innovation: Speciation and Morphogenesis, The MIT Press, ISBN 0-262-13269-9 (《共生作為演化創造力的來源:物種形成與形態發生》)
Margulis, Lynn and Dorion Sagan, 1991, Mystery Dance: On the Evolution of Human Sexuality, Summit Books, ISBN 0-671-63341-4 (*《性的歷史》)
Margulis, Lynn and Dorion Sagan, 1987, Microcosmos: Four Billion Years of Evolution from Our Microbial Ancestors, HarperCollins, ISBN 0-04-570015-X (*《演化之舞:細菌主演的地球生命史》)
Margulis, Lynn and Dorion Sagan, 1986, Origins of Sex : Three Billion Years of Genetic Recombination, Yale University Press, ISBN 0-300-03340-0 (《性的起源:三十億年來的遺傳重組》)
Margulis, Lynn, 1982, Early Life, Science Books International, ISBN 0-86720-005-7 (《早期生命》)
Margulis, Lynn, 1970, Origin of Eukaryotic Cells, Yale University Press, ISBN 0-300-01353-1 (《真核細胞的起源》)