Objective：To investigate the distribution of the subtype of Treponema pallidum（TP） in Chongqing，and to explore the clini－cal correlation of genetype. Methods：Four hundred twenty one specimens were collected from patients with seropositive syphilis from June 2010 to October 2013，and were screened by nested PCR targeted TP DNA polymerase I gene（polA）. The acid repeat pro－tein（arp），treponema pallidum repeat（tpr） and TP0548 genes were amplified with the positive specimens above. Then the strains were subtyped according to Pillay’s criteria and subtyping method of targeted three genes. Analysis was made concerning the correla－tion of different genetypes with sero-resistance，syphilis recurrence and Jarisch-Herxheimer reaction by Fisher’s exact test，respec－tively. Results：Totally 163 specimens were positive by PCR targeted polA gene. Of 116 TP positive specimens subtyped by arp，sub－type 14 was the predominate genotype，while of 114 specimens subtyped by tpr gene，d was the most common genotype. Of 117 specimens subtyped by TP0548 gene，subtype f was predominate. At 12 months after standard treatment，32 patients occurred sero-re－sistance including 11 subtype d，2 subtype b，2 subtype a and 1 subtype f. Three patients experienced syphilis recurrence including 2 TP0548 subtype c and 1 subtype f. Eight patients developed Jarisch-Herxheimer reaction，including 4 genotype 14f/f，3 geno－type 14d/f and 1 patient failing to subtype. There were statistical differences in the correlation of molecular subtypes with sero-resis－tance and Jarisch-Herxheimer reaction（P=0.000，P=0.029），while no statistical difference of the correlation of genetypes with syphilis recurrence was found（P=0.333）. Conclusion：The predominate subtypes of TP in Chongqing is subtype 14，d and f. It is suggested that the sero-resistance be related with TP tpr subtype b and the second satge syphilis with 14f/f is more likely to develop a Jarisch-Herx－heimer reaction following benzathine penicillin treatment.