The objective of this study was to assess the distribution of Chlamydia trachomatis genovars in male sexually transmitted disease (STD) clinic patients from 1 province in eastern China (Jiangsu) and 3 provinces in southern China (Guangdong, Guangxi, and Hainan). Urine specimens (n = 140) were collected from 46 public STD clinics in the 4 provinces. Specimens that tested positive for C. trachomatis by polymerase chain reaction were genotyped for the infecting C. trachomatis strain by amplifying and sequencing the genovar-specific ompA gene, which encodes the chlamydial major outer-membrane protein. Nine C. trachomatis genovars were identified from 129 specimens; they consisted of the F (25.6%), E (17.1%), J (16.3%), D (15.5%), G (11.6%), K (5.4%), H (3.9%), I (1.6%), and B (0.8%) genovars. Nine genovars were found in specimens from Guangxi province, 6 were found in specimens from each of Guangdong and Hainan provinces, but only 5 were found in specimens from Jiangsu province. Genovar G/Ga was shown to be endemic among male patients in southern China.