Abstract: Objective In order to support the bacterial pathogen identification and classification in communicable disease control and prevention as well as clinical treatment, an online bioinformatic analysis platform was established based on a merged and non-redundant 16S rDNA database. Methods To build the comprehensive, accurate and non-redundant 16S rDNA database,16S rDNA sequences of known bacteria in the open international databases, including RDP, GenBank, SLIVA, HOMD were collected and rearranged. A bioinformatic pipeline was established for bacterial pathogen identification and classification using common bioinformatic software and PERL programming language, and an automatic online platform was developed using web 2.0 and JAVAEE technology. Results A total of 1 450 265 16S rDNA sequences were collected and 96 138 sequences were kept in the database. An online system was established including sequence alignment and clustering functions(http://ssu.bioinfo-icdc.org). Conclusion This platform could be used in the rapid and accurate identification and classification of pathogenic bacteria by analyzing the 16S rDNA sequence online fleetly and simply, which can simplify the procedures and speed the process of communicable disease control and treatment.