Abstract:High-throughput bacterial species identification is an important research topic in the area of microbiology, which plays a pivotal role in the disease diagnosis and environmental monitoring. Compared to the traditional phenotypic identification methods, molecular methods have the features of higher stability, shorter detection period and lower cost, which are becoming the main trend in the bacterial species identification. Especially, next generation sequencing technique, the detection chips based on nucleic acid identification, the protein profile analyses based on mass spectrometry provide the valid means for high-throughput, fast, accurate and quantitative bacterial species identification.