Intrauterine transmission of hepatitis B virus (HBV) is one of the main reasons for the failure of vaccination and plays an important role in areas with high HBV prevalence. In the present study, the quasispecies isolated from eight pairs of HBsAg-positive mothers and their neonates, who were infected with HBV by intrauterine transmission, were selected as study subjects. Phylogenetic trees of the HBV strains of each pair of mother and neonate were constructed, the topological structures were compared, and the distance between and within the quasispecies was calculated. The eight phylogenetic trees included four types. In the first type, the maternal and neonatal sequences clustered into one clade. In the second type, the sequences of the mothers and neonates formed separate monophyletic clusters, and the two clades were sister groups. In the third type, the strains of mother were the ancestors of the neonatal strains. In the fourth type, the strains of the mothers clustered with only some of the sequences of the neonate, and the other strains of the neonate formed another monophyletic group. Combined with the genetic distance, possible transmission routes of the eight cases are proposed.