In upstream reaches of the Tama River, musty odor substance (2-methylisoborneol (2-MIB)) began to be detected in 2008 and the concentration has been increasing thereafter. Then, in 2012, 2-MIB in raw water of a water treatment plant reached 210 ng/L. It was suspected that cause of musty odor was benthic cyanobacteria ( Phormidium ) which attached to stones on the riverbed. However, identification of the benthic Phormidium by microscopic observation had been difficult, thus genetic analysis was carried out. In genetic analysis, almost full-length 16S ribosomal DNA and internal transcribed spacer region gene of benthic Phormidium strains, which include the strain isolated from the Tama River, a strain in the Yoshino River (350 km away from the Tama River) and standard strains, were sequenced and compared. From homology search of these sequences, 2-MIB producing Phormidium in the Tama River was classified into Phormidium autumnale . Furthermore, it was found that P . autumnale in the Tama River was the same species in the Yoshino River. In addition, the result of in vitro cultivation shows that the P . autumnale inhabiting the Tama River thrives and produces more 2-MIB at high temperature, but it can grow and produce 2-MIB even at low temperature.