Hepatitis B virus genotypes are associated with transmission pattern, virological and clinical features and outcome of the chronic infection course. HBV genotypes other than Genotype F (HBV/F) are considered a reflection of human migration into South America. A total of 487 individuals in Bolivia, including Japanese immigrants (n=287) and natives (n=200), were screened for HBV serological markers. Overall 22/487 (4.5%) of the subjects were positive for HBsAg, 217/487 (44.5%) for anti-HBc and 162/487 (33.3%) for anti-HBs. Genotypes were determinable in 22 cases by EIA, followed by sequencing and phylogenetic analysis in 17 cases. HBV genotype distribution in Japanese and Bolivians was HBV/F (4 and 8); HBV/C (5 and 3); and HBV/B (1 and 1), respectively. Phylogenetic analyses of nine complete and eight partial (HBsAg/pre-core/core region) genomes, revealed that HBV/F strains cluster with previously reported regional strains, whereas HBV/B and HBV/C strains belonged to Asian subgenotype B2 (Ba) and C2 (Ce), respectively. Japanese immigrants might have introduced HBV/B and HBV/C to natives in Bolivia, conversely, exposed to the indigenous HBV/F. This report provides evidence of an inter-communities transmission of HBV revealed by its genotypes. Further study is required to investigate peculiarities of the genotypes in different ethnic groups in Bolivia.