Abstract: Objective To establish an online bioinformatics analysis system based on browser/server model and apply it in communicable disease control and prevention. Methods We collected 15 client/server model bioinformatics software widely used in pathogenic microorganism research and molecular diagnosis of communicable disease to establish a bioinformatics analysis system that require no installation of software on user’s computer and could be used on line through internet browser. Results An online analysis system, including 4 groups of software used for primer design, sequence alignment, phylogenetic tree building, data statistics and graph construction, was developed and applied. Conclusion This online bioinformatics analysis system can provide more convenient and rapid bioinformatics service for researchers working in communicable disease control and prevention, speed up the analysis of pathogenic microorganism sequence data and infectious source tracing as well as improve the response to public health emergency.