Hepatitis B virus (HBV) genotype E is highly prevalent in the Western part of sub-Saharan Africa, where it shows an extensive geographic spread, but a low genetic diversity. In Haiti, where more than 90% of the population are descendants of African slaves, HBV genotype E was very rare, suggesting that this genotype may not have been present in the population when and where the slaves were rounded up. To further test this hypothesis, we performed genotyping on serum samples of 172 HBV-DNA positive patients from Cuba. Based on phylogenetic analysis of the S gene, the by far most prevalent genotype was A (92.4%, subgenotypes A1 and A2), followed by genotypes D (7.0%) and C (0.6%). No genotype E sequences were found. Part of the current Cuban population are descendants of African slaves who originated mostly from the Gulf of Guinea and the South of Angola, both regions that belong to the genotype E crescent. Thus, the absence of genotype E in Cuba further corroborates the theory that HBV genotype E may have emerged in the general population in Africa only after the transatlantic slave and thus within the last 200 or 300 years. While these findings explain the low genetic diversity of genotype E, its vast spread throughout Western Africa may be due to an extensive use of unsafe needles in injection mass campaigns during the colonial era.