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Consumers often complain about taste and odor (T&O) in drinking water and freshwater fishery. One of the common T&O compounds, 2-methylisoborneol (2-MIB), can be detected by humans even when the concentration is below 10 ng/L. A forecast method of T&O occurrence is required to control drinking water plants and fishery farms to determine the timing of exchange of activated carbon or exchange the water in earthy pond. Traditional monitoring methods such as PCR, microscopy, and chemical analysis require a long time, are high in cost, and have a complex operation. We conducted this study to develop whole-cell PCR and whole-cell qPCR assays for rapid detection and quantification of 2-MIB-producing cyanobacteria without DNA extraction to detect 2-MIB cyclase gene (mtc). Pseudanabaena foetida strain 1705-12 (Lake Kasumigaura), strain 1803-12 (Lake Kasumigaura), and strain PTG (Lake Biwa) of 2-MIB-producing cyanobacteria were used in the study. The positive correlation between the results of whole-cell PCR, whole-cell qPCR and chlorophyll a (Chl.a), and gene abundances illustrated that whole-cell PCR and whole-cell qPCR assays could rapidly and conveniently detect and quantify 2-MIB-producing cyanobacteria. Thus, this study provides a valuable tool for prediction of T&O events in drinking water and freshwater fishery.