Characterizing the impact of HIV transmission routes on viral genetic diversity can improve the understanding of the mechanisms of virus evolution and adaptation. The HIV vertical transmission can occur in utero, during delivery or while breastfeeding. The present study investigated the phylodynamics of the HIV-1 env gene in mother-to-child transmission, by analyzing one chronically infected pair from Brazil and three acutely infected pairs from Zambia, with three to five time points. Sequences from 25 clones from each sample were obtained and aligned using Clustal X. ML trees were constructed in PhyML using the best evolutionary model. Bayesian analyses testing the relaxed and strict molecular clock were performed using BEAST and Bayesian Skyline Plot (BSP) was construed. The genetic variability of previously described epitopes were investigated and compared between each individual time points and between mother and child sequences. The relaxed molecular clock was the best-fitted model for all datasets. The tree topologies did not show differentiation in the evolutionary dynamics of the virus circulating in the mother from the child viral population. In the BSP, the effective population size was more constant along the time in the chronically infected patients while in the acute patients it was possible to detect bottlenecks. The genetic variability within viral epitopes recognized by the human immune system was considerably higher among the chronically infected pair in comparison with acutely infected pairs. These results contribute to the better understanding of the HIV-1 evolutionary dynamics in mother to child transmission.