Hepatitis B virus (HBV) infection is considered as the fifth leading cause of death due to infectious diseases and has a worldwide prevalence. The particular geographical distribution of the eight previously defined genotypes of HBV suggests that the viral population is highly structured. The presence of such population structure is likely to affect the geographical distribution of polymorphisms involved in disease progression. In this study, we determined the structure of the HBV population using a clustering approach based on the observed allele frequencies at the polymorphic loci. We used all full-genome sequences publicly available and obtained a significant clustering of the HBV population into four main clusters, strongly associated with the current classification into genotypes. One of these main clusters could itself be split into three well-supported subclusters, highlighting the hierarchical nature of the population differentiation between HBV strains. The extremely clear-cut subdivision of the HBV population further indicates that recombination in HBV is not as extensive as previously assumed.