Reason for the genetic differences between humans and Neanderthals is that the two populations were separated for a long period of time, and evolved independently. Humans and Neanderthals likely diverged from a common ancestor around 600,000 years ago, and lived in separate geographic regions for hundreds of thousands of years.

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During this time, the two populations were exposed to different selective pressures, which led to the evolution of distinct physical and behavioral adaptations.Another reason for the genetic differences between humans and Neanderthals is that there was some interbreeding between the two populations. Studies of the Neanderthal genome have revealed that modern humans of non-African descent carry about 2-4% of Neanderthal DNA in their genome, indicating that there was some interbreeding between the two populations when modern humans first began to migrate out of Africa.

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Comparing two human individuals, the genetic differences would be much smaller. The human genome is about 99.9% identical from person to person, with the remaining 0.1% accounting for genetic variation that is responsible for differences in physical characteristics, such as eye and hair color, as well as differences in susceptibility to certain diseases.