A novel approach to the identification of microorganisms that accumulate high density microbial storage products based on density separation, denaturing gradient gel electrophoresis (DGGE), and DNA sequencing was developed and applied to bench and pilot scale enhanced biological phosphorus removal (EBPR) systems. Polyphosphate (PP), glycogen, and polyhydroxyalkanoates (PHAs), are all of higher density than a typical bacterial cell. PP-accumulating organisms (PAOs), the organisms responsible for EBPR, accumulate all three of these storage products. Density separation in a homogenous solution of Percoll produced a high-density biomass fraction with a relatively high concentration of PAOs, as determined by Neisser staining. DNA was extracted from these fractions, amplified, and separated by DGGE. DGGE profiles demonstrated some bacterial strains were present at a greater concentration in the high density fractions than in low density fractions. These strains were considered PAO candidates. 5 of 12 PAO candidates from high density fractions were gamma Proteobacteria and only 1 was a beta Proteobacterium. 2 PAO candidates were most similar to recently identified gamma Proteobacteria sequences obtained by DGGE analysis of a deteriorated benchtop EBPR system.