Background and Aim: The prevalence of genotype of hepatitis C virus (HCV) is an important test in clinical epidemiology as well as in the treatment of HCV carrier with combined interferon and ribavirin. Response rate of treatment is related to the genotype of HCV. This study is to further investigate the different prevalence of HCV genotype between IVDU and non-IVDU. Method: from July. 2003 to June 2005, 479 cases of viral hepatitis C were included in this study, 281 cases were IVDU and 198 were non-IVDU. Direct purification of HCV viral nucleic acids from serum with QIAmp Viral RNA Mini Kit (QIAGEN); LightCycler RNA Amplification Kit SYBR Green I, Roche was used to detect the genotype of HCV. Result: the prevalence of HCV genotype 1 in IVDU group was 40.56% ( 1a: 20.28%, 1b: 20.28%), genotype 2 59.44%( 2a: 46.98%, 2b: 12.46%); but in non-IVDU group genotype 1 occupied 61.12%( 1a: 3.54%, 1b: 57.58%), genotype 2 was 36.87%(2a: 25.25%, 2b: 11.62%). Conclusion: the prevalence of genotype 1b of HCV was predominant in non-IVDU group, but 2a in IVDU group.