A useful method to identify hop varieties by genomic analysis is presented. Utilizing the simplicity of the random amplified polymorphic DNA (RAPD) procedure, genetic markers for the identification of hop varieties were screened. To make up for the deficiencies of RAPD, specific primers were designed based on the sequences of the RAPD markers. Twelve typical hop varieties were successfully distinguished using these specific primers. The method was also successfully used for the detection of the mixed samples.