With the increasing occurrence of water eutrophication and blooms, earthy-musty odor problems caused by cyanobacteria have been more and more apparent. These problems have a serious impact on aquatic ecosystems and drinking water safety and become one of the priorities of the water environment researches and managements. In the present study, genes associated with 2-MIB synthesis in cyanobacteria were studied by systematic investigation on molecular characterization and quantity of 2-MIB-producing cyanobacteria in China. Our results founded that Pseudoanabaena is an important 2-MIB-producing phytoplankton and predominant in summer in Qingcaosha reservoir, and the copy number of mic and 2-MIB concentration have strongly positive correlation. We also demonstrated that abundance of mic in water was significant correlation with that in sediment. These results will help us to understand the main taxa of the odoriferous cyanobacteria in the water bodies in China, understand the genetic basis of the odor substances in the cyanobacteria. Rapid, reliable monitoring and ecological research methods for the production of odor cyanobacteria in water bodies can be established based on these results.