Abstract: Objective To examine the application of polymerase chain reaction(PCR)method in diagnosis of pertussis and to explore molecular epidemiological features of pertussis. Methods Totally 110 suspected pertussis cases were selected and their nasopharyngeal swabs were sampled at hospitals or community monitoring settings in Tianjin.Genetic screening of Bordetella pertussis gene was conducted with PCR and ELISA was used to detect specific pertussis toxin(PT)-IgG antibody. PTS1 subunit gene region in pertussis DNA positive samples was sequenced and analyzed. Results The PCR positive rate was 60%in 110 suspected pertussis cases and the PT-IgG antibody positive rate was 42.55%in 94 suspected pertussis cases.PCR positive rate was significantly higher than that of PT-IgG antibody(χ²=6.181,P=0.013).The PCR detection rate was significantly higher in the cases less than one year old than in the cases of other age groups.All DNA gene 19 Bordetella pertussis strains were closely related with a nucleotide homology of 99.88%.In the S1 subunit of PT region,amino acid 218 mutated from methionine(Met)to isoleucine(Iso)(Met218→Iso218). Conclusion PCR detection of clinical nasopharyngeal swab sample for diagnosis of pertussis is sensitive and convenient.The Bordetella pertussis prevalent in Tianjing is closely related in gene homology.