Polyphosphate-accumulating microorganisms(PAOs) plays key roles in enhanced biological phosphorus(P) removal. Intracellular polymers, including polyphosphate(poly-P), polyhydroxyalkanoates(PHAs) and glycogen, were proved to have close relations with PAO's metabolism. PAOs storage polymers can be identified and quantified by many methods. In this paper, a variety of methods were used to dye PAOs' storage polymers. Results showed that Nile Blue staining was more specific than Sudan black staining to the PHB in anaerobic stage, and to the poly-P in aerobic, DAPI staining and Neisser new staining were proper than others.