Suncus murinus is gaining prominence as a laboratory animal; however, there is no generally accepted method for microbiological monitoring. This study aimed to apply non-serological microbiological monitoring of laboratory mice for S. murinus and identify the subdominant species obtained by culture methods for microbial assessment. Culture and PCR were used to test S. murinus for the laboratory mice test panels including 10 bacterial species and orthohantaviruses, all of which were negative. The species that grew sub-dominantly in rectal feces were identified as Aeromonas hydrophila, which is pathogenic to mammals. These results indicate that microbiological monitoring should be used to detect pathogens directly from S. murinus, not from sentinel animals, due to the host-specific microbial environment.