Activated sludge bulking caused by filamentous bacteria Eikelboom type 021 N and Thiothrix spp. is reported for the first time in a multistage pilot-scale wastewater treatment plant for enhanced biological phosphorus removal (EBPR). Both types of microorganisms grew gradually reaching their maximum cumulative length within a period of 2 months. For identification of the strains, in addition to physiological observations under the microscope, Gram staining, Neisser staining and sulfur storage test took place. Results confirmed that biological nutrient removal systems may also suffer from sludge bulking. Plant configuration, wastewater composition, removal efficiency and filaments' growth stages were examined in relation to the occurrence of the certain strains in an EBPR system.