Phosphorus is one of the nutrients can causing eutrophication of lakes, inland seas and other natural waters, which threaten the safety of drinking water systems and ecological risk. Removal of phosphorus from wastewater is therefore important for preventing eutrophication. Nowadays, enhanced biological phosphorus removal (EBPR) has been broadly applied in wastewater containing phosphorus treatment because of its lower cost and more environmental friendly technology compared to chemical precipitation or adsorption 1. Different from chemical or physical treatment methods, EBPR, like other biological wastewater treatment systems, depends on the metabolism of microbial communities to remove phosphorus, possibly removing simultaneously organic or inorganic pollutants. Moreover, EBPR systems are difficult to control and deteriorate in the performance of phosphorus removal 2. So, a better understanding of microbial communities in EBPR system can give important guidance in design or reconstruction and stable operation of EBPR process 3-5. Many molecular techniques used for microbial community analysis have been rapidly developed during the past decade, including polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) 6,7 , fluorescence in situ hybridization (FISH) 8-10 , terminal restriction fragment length polymorphism (T-RFLP) 11 and clone library 12 .