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Background: The CRISPR/Cas9 system is being used for genome editing purposes by many research groups in multiple plant species.Traditional sequencing methods to identify homozygous mutants are time-consuming,laborious and expensive.Results: We have developed a method to screen CRISPR/Cas9-induced mutants through Mutation Sites Based Specific Primers Polymerase Chain Reaction(MSBSP-PCR).The MSBSP-PCR method was successfully used to identify homozygous/biallelic mutants in Nicotiana tabacum and Arabidopsis thaliana,and we speculate that it can be used for the identification of CRISPR/Cas9-induced mutants in other plant species.Compared to traditional sequencing methods,MSBSP-PCR is simpler,faster and cheaper.Conclusions: The MSBSP-PCR method is simple to implement and can save time and cost in the screening of CRISPR/Cas9-induced homozygous/bialleic mutants.