Objective To set up microbial community-level physiological fingerprint profiling database in four different aquariums feeding zebrafish, analyze and assess whether micropathogens infect zebrafish during standard raising. Methods MicroStation microbial identification system was used. Microbial community utilized 95 compounds for carbon source on identification microplate. When microbial pathogens utilized carbon substances in a well, respiration lead change of oxidation and deoxidized indicator, and color change becomes identification fingerprint. Result In this experiment, 22 carbon sources on GN and GP microplates were utilized by all of healthy microbial community in zebrafish aquariums based on multivariable analysis. Conclusion This approach, called community-level physiological profiling (CLPP), has been effective for distinguishing healthy and pathogenic microbial communities in the aquariums, and provided a set of healthy fingerprint database.