University of Waikato 1 article published in JoVE Genetics Measuring Microbial Mutation Rates with the Fluctuation Assay Rok Krašovec1, Huw Richards2,3, Guillaume Gomez3, Danna R. Gifford1, Adrien Mazoyer4, Christopher G. Knight3 1School of Biological Sciences, The University of Manchester, 2School of Science, University of Waikato, 3School of Natural Sciences, The University of Manchester, 4Department of Mathematics, Université du Québec à Montréal Here, a protocol is presented to perform a fluctuation assay and estimate microbial mutation rate using phenotypic markers. This protocol will enable researchers to assay mutations in diverse microbes and environments, determining how genotype and ecological context affect spontaneous mutation rates.