Filamentous bulking, the most common solids separation problems in wastewater treatment systems, is caused by filamentous bacteria extending outside the flocs. Previous studies using microscopy and conventional molecular techniques, such as fluorescence in situ hybridization and real-time qPCR, have difficulty in obtaining the complete profile of filaments. In this study, metagenomic analysis using an Ion Torrent Personal Genome Machine (PGM) platform was adopted to investigate the filamentous bacteria community in Macau wastewater treatment plant that is experiencing filamentous bulking in recent years. The results showed that approximately 571 MB bases of raw data were obtained, acquiring a total of 561,943,741 clean and high-quality bases for further subsequent analysis. Haliscomenobacter hydrossis was identified as the dominant filaments that caused bulking. The present study indicated that the total filamentous bacteria could be determined well through PGM sequencing, from which the oligonucleotide probes and primers can be developed and used for targeting the interest species under different operational conditions. In addition, the distributions of Virus, Bacteria, Archaea, Eukaryote domain at read and contig level were determined in this study.