Recent methodological advances have increased the pace and scale of African ancient DNA (aDNA) research, inciting a rush to sample broadly from museum collections, and raising ethical concerns over the destruction of human remains. In the absence of discipline-wide protocols, teams are often left to navigate aDNA sampling on an individual basis, contributing to widely varying practices that do not always protect the long-term integrity of collections. As those on the frontline, archaeologists and curators must create and adhere to best practices. We review ethical issues particular to African aDNA contexts and suggest protocols with the aim of initiating public discussion.