Currently, researchers use bacterial culture and targeted PCR methods to classify, culture, and identify the pathogens causing abscess diseases. However, this method is limited by factors such as the type of culture medium and culture conditions, making it challenging to screen and proliferate many bacteria effectively. Fortunately, with the development of high-throughput sequencing technology, pathogen identification at the genetic level has become possible. Not only can this approach overcome the limitations of bacterial culture, but it can also accurately identify the types and relative abundance of pathogens. In this study, we used high-throughput sequencing of 16S rRNA to identify the pathogens in purulent fluid samples. Our results not only confirmed the presence of the main pathogen reported by previous researchers, Trueperella pyogenes, but also other obligate anaerobes, Fusobacterium necrophorum and Bacteroides fragilis as the dominant pathogens causing abscess diseases for the first time. Therefore, our findings suggest that high-throughput sequencing technology has the potential to replace traditional bacterial culture and targeted PCR methods.