The application of Fluorescence In-situ Hybridization (FISH) to research of biological removal of nitrogen and phosphorous from wastewater was discussed after a brief introduction of its principal theory.Though there exists close relationship between macroscopical performance of biological removal of nitrogen and phosphorous and the state of microorganism, the sort, quantity and structure of microbes inside the wastewater treating system had not been well understood yet because of lack of proper examining technology.The research shows that FISH can provide an excellent examining method for identification and sub-classification of polyphosphate accumulating organisms (PAO) and nitrifying bacteria.Moreover, the combination of FISH with other methods such as polymerase chain reaction (PCR) can make it more powerful.