Studying ancient pathogens is critical to improve our understanding of modern epidemics and the evolutionary processes that govern them. However, determining the authenticity of ancient DNA (aDNA) samples is difficult. Here, I will describe a hepatitis B virus recovered from a 16th century mummy. Statistical analysis of the damage patterns indicated an authentic pattern of degradation as expected for aDNA, however the phylogenetic analysis indicated that the virus was closely related to modern samples. Moreover, molecular clock analyses were inconclusive in estimating the age of this sample. A probable explanation for this paradox is that this close relationship is due to saturation by reverse mutation leading to loss of the phylogenetic signal over the time frame of several hundred years. This study presents a phylogenetic framework that may be used for determining the robustness of age estimates in aDNA work.