Objective: To investigate the molecular epidemiology of hepatitis C virus (HCV) among drug users in Zhuhai, China. Methods: Anti-HCV and HCV RNA were detected by using ELISA and real-time RT-PCR respectively. HCV genotypes and subtypes were determined by direct sequencing of amplicons in partial NS5B regions and BLAST GenBank, followed by phylogenetic analysis. Results: Of 435 blood plasma from drug users, 242 was negative for anti-HCV and HCV RNA, 147 were positive for anti-HCV and HCV RNA, 46 positive HCV RNA or anti-HCV. The infection rate of HCV was 44.37%. Three genotypes and five subtypes of HCV were detected in 78 samples of positive HCV RNA. Subtypes 6 a, 3b, 3 a, 1b and 1 a, were detected at frequencies of 60.26%, 15.38%, 14.10%, 6.41% and 3.85%, respectively. Compared with strains from Shenzhen, Foshan, Guangzhou, Shanwei, Hong Kong, Denmark, Canada, USA, United Kingdom, India and Nepal, HCV among drug users in Zhuhai were homophylic. Conclusions There were homology among HCV in drug users from Zhuhai and strains from some regions and countries. Subtype 6 a was the most predominant. Subtype 1 a and 3 a were discovered in Zhuhai.