Flow cytometer, an advanced instrument integrating fluidics, optics, electronics, biology, immunology, etc., measures cells in suspension that flow in single-file through laser beam. Flow cytometry (FCM), as the core of flow cytometer, is a multidisciplinary technique for analysing and sorting cells or other particles. FCM can provide a multitude of information at the single-cell level, including (but not limited to) total counts, size measurements, nucleic acid content, cell viability and activity, and detection of specific bacterial groups or species. The main advantage of FCM is that it is fast, sensitive, accurate and easy to perform. Here, we briefly review the basic principle of flow cytometer, focusing on its recent applications to rapid detection of bacteria in laboratory research, industrial biotechnology, clinical diagnosis and environment assessment.