With a deep history of occupation dating back millennia and home to the first kingdoms of the African continent, the northeast region of Africa, namely the Nile River Valley, is a fascinating place to explore human history. The genomic diversity of human populations has been the subject of decades of research and now the more ancient inhabitants of this region are the new focus. Ancient DNA provides a valuable new line of evidence to supplement and reexamine hypotheses built upon archaeological, historical, and anthropological data to understand past population dynamics. African samples have proven to be more problematic than those from more temperate environments and method optimization has been vital to access DNA from archaeological samples. Here, I will present these trials and the first reconstructed genomes of ancient Nubians (or modern-day Sudan) from the Middle Nile Basin.