Background/Aims: Hainan Island has been inhabited by the “Li” aboriginal minority for centuries where the HCV genotype distribution patterns maybe remarkably different from other parts of China. We aimed to provide a better understanding of the infection with HCV genotype 6 among “Li” aboriginals on Hainan Island. Methods: Firstly, using RT-PCR and DNA sequencing to determined 517 partial HCV Core-E1(115 from Li Ethnic, 402 from Han Ethnic) and 8 full-length genomes from Li ethnic in Hainan Island successfully, and then using the phylogenetic tree to determine the HCV genotype distribution and analyze the evolution of them. Results: Phylogenetic tree analysis showed that the distribution pattern of HCV genotypes among the Han and Li ethnic population exhibits significant diferences: 6a was the most prevalent subtype in Han ethnic of Hainan Island followed by 1b, 3b, 2a, 3a, and 1a. All genomes from Li ethnic were classified into genotype 6, while 84 out of 115 (73%) could not be classified. Nine sequences (HN1350 et al.) from Li ethnic might be assigned to a new subtype 6xh as their p-distances ranged from 5.9∼9.7%. Furthermore, we sequenced and characterized full-length genomes for eight HCV-6 isolates which were all from Li ethnic in Hainan Island. Among these isolates, the HN1350 was classified as a new subtype: 6xh. Conclusion: Overall, we firstly defined a new subtype of genotype 6xh through partial and new full length genome. And we found a unique distribution pattern of HCV 6 in the Li tribe, which might provide a better way to understand the genetic diversity of HCV-6 and to investigate the phylogeny of HCV strains from Li tribe.