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To identify the genomic species of Neisseria gonorrhoeae, evaluate the difference between two molecular epidemiological methods and examine the relationship between sex partners and genotypes of bacteria, 24 strains of Neisseria gonorrhoeae isolated from the outpatients with gonorrhea were identified by using the Opa genotyping and NG-MAST genotyping and the relationship between genotypes and phenotypes was studied. Twenty-four strains of Neisseria gonorrhoeae fell into 10 ST genotypes by NG-MAST genotyping, whereas these strains were classified into 12 OT Opa genotypes by Opa genotyping. A new epidemic strain of ST genotype (217-86% homologisation 178) in China was identified. It is concluded that genotypes of each pair of strains from a pair of patient/sex partner besides 45/46 are the same, indicating that contagious infection take place between patient and the sex partner. Opa genotyping was more effective than NG-MAST genotyping in identifying the genomic species of Neisseria gonorrhoeae. ST genotype could be further classified into different Opa-types.