Michael Lynch's research is on the mechanisms of evolution on genes. His analysis of how genes are altered and damaged in Daphnia and Paramecium. As a professor for the School of Life Sciences and the center director for the Biodesign Center for Mechanisms and Evolution, his work also spans the origins of cellular features, noting possibilities for phylogenetic relationships as well as the evolution of cellular features in complex organisms.

Lynch has served as President of the Genetics Society of America, the Society for Molecular Biology and Evolution, the Society for the Study of Evolution, and the American Genetic Association. He is also a member of the U.S. National Academy of Sciences, and a fellow of the American Academy of Arts and Sciences.