The Neanderthal genome project is an effort of a group of scientists to sequence the Neanderthal genome, founded in July 2006.

It was initiated by 454 Life Sciences, a biotechnology company based in Branford, Connecticut in the United States and is coordinated by the Max Planck Institute for Evolutionary Anthropology in Germany. In May 2010 the project published their initial draft of the Neanderthal genome (Vi33.16, Vi33.25, Vi33.26) based on the analysis of four billion base pairs of Neanderthal DNA. The study determined that some mixture of genes occurred between Neanderthals and anatomically modern humans and presented evidence that elements of their genome remain in modern humans outside Africa.

In December 2013, a high coverage genome of a Neanderthal was reported for the first time. DNA was extracted from a toe fragment from a female Neanderthal researchers have dubbed the "Altai Neandertal". It was found in Denisova Cave in the Altai Mountains of Siberia and is estimated to be 50,000 years old.