In recent years, the molecular methods using short tandem repeats sequences in microbial genome to design primers and amplify the sequences have been continuously reported. The PCR based on the BOX elements is a simple, fast, highly reproducible method for comparing patterns of the amplified bands, and it was applied in studies on the classification of bacteria originally. Researchers found that it could be used as well for analysis of the genetic diversities of fungi and streptomyces using BOXA1R primer to amplify the BOX elements. This paper reviewed the characteristics and the general procedure of BOX-PCR fingerprinting. The system optimization of BOX-PCR fingerprinting for endophytic bacteria and BOX-PCR technology improvements are summarized. Its applications and prospect on diversity research of different microorganisms are discussed as well.