Background and Aims: Hepatitis C virus (HCV) genotype (GT) 6 is the most genetically diverse GT and mainly distributed in Southeast Asia and south China but not Taiwan. Earlier studies showed the major GTs in Taiwan were GT 1b and GT 2 with very rare GT6 except in injection drug user and subtype 6a is the main GT 6 subtype among IDUs. Recently we reported a much higher prevalence (18.3%) of GT 6 in Tainan City, southern Taiwan. This study was designed to clarify the subtypes of GT 6 in this endemic area. Materials and Methods: A total 3022 (1343 men and 1679 women) HCV patients were enrolled. GT 6 subtypes were determined by sequencing of core/E1 and nonstructural protein 5B (NS5B) in 322 of 518 GT 6 patients. Results: The overall GT6 prevalence rate was 17.1% (518/3022) with higher prevalence districts located in northern Tainan. The major GT6 subtypes in Tainan were 6g (81.0%), followed by 6w (10.8%), 6a (7.5%), and 6n (0.7%).Conclusions: The high GT 6 prevalence in Tainan was mainly due to subtype 6g and 6w with characteristic geographic distribution, suggesting subtypes 6g and 6w could be indigenous in Tainan for centuries.