Projection analysis is a useful tool for understanding the relationship of two populations. It compares a test genome to a set of genomes from a reference population. The projection’s shape depends on the historical relationship of the test genome’s population to the reference population. Here, we explore the effects on the projection when ancient samples are included in the analysis. First, we conduct a series of simulations in which the ancient sample is directly ancestral to a present-day population (one-population model) or the ancient sample is ancestral to a sister population that diverged before the time of sampling (two-population model). We find that there are characteristic differences between the projections for the one-population and two-population models, which indicate that the projection can be used to determine whether a test genome is directly ancestral to a present day population or not. Second, we compute projections for several published ancient genomes. We compare three Neanderthals, the Denisovan and three ancient human genomes to European, Han Chinese and Yoruba reference panels. We use a previously constructed demographic model and insert these seven ancient genomes and assess how well the observed projections are recovered.