根据一些资料来源，测序人类DNA的过程不是一个确定的过程。据说人类化石中所含的DNA被污染，有时没有足够的足够进行足够的基因比较。然而，在莱比锡的马克斯普朗克研究所，德国在现代技术的帮助下成功的DNA序列的尼安德特人与现代人类的DNA进行比较。即使机器使用和使用的方法被称为不完美，他们设法破译尼安德特人DNA三分之二和想出的统计，百分之四的现代人的DNA是相似的人。然而，该研究并没有指出任何人的特性，可以直接归因于尼安德特人，有研究表明现代人的头盖骨的发展过程可以被归因于尼安德特人但没有事实支持这一理论（Trinkaus 2007）。对近代早期欧洲的人的特征与尼安德特人使用已记录的古生物资料显示有现代欧洲早期人类和尼安德特人之间的相似特征的比较（Trinkaus 2007）。然而同样的相似性不追溯到旧石器时代中期的现代人类（mpmhs）从他们的早期欧洲现代人据称来自（Trinkaus 2007）。这意味着，必须要有来自非洲的欧洲早期现代人类的迁移过程中被遗传交换（Trinkaus 2007）。
There has been a hot debate recently about the relationship between the human species and the Neanderthals (The first European were Khoisan 2010). The species are very much related that some researchers and scientists have termed them as the same species. "I would see them as a form of humans that are bit more different than humans are today, but not much," Said Pablo, scientist whose research team conducted a sequence on the Neanderthal man genome (Max Planck Institute for Evolutionary Anthropology 2010),
According to a recently conducted deoxyribonucleic acid test, human beings exhibit some Neanderthal characteristics (Max Planck Institute for Evolutionary Anthropology 2010). The study shows that, in every human being who does not have an African ancestral there is about one to four percent of the genetic makeup matches with the genetic makeup of the Neanderthal (Max Planck Institute for Evolutionary Anthropology 2010),. The Neanderthal who is believed to have died around 30000 years ago is believed to have interbred with the modern man (Homo sapiens). Some study shows that the mating took place somewhere in the Middle East after the modern man had started his migration from Africa to Europe. Comparing the genetic characteristics of the modern early man in Europe and the morphological characteristics of the immediate remains there is a genetic rhyme of the genes with the genetic characteristics of the initial (Early) African modern man. However, there is some variation in the characteristics; the characters which differ between the African Early man and the European early man are deemed to be Neanderthal. The varying characteristics included features such as, the dental structure, external body structure and the overall neurocranial shape. In a prepared statement, lead study author Ed Green of the University of California, Santa Cruz said that in all probability, there must have been a gene flow from Neanderthals to this day human.
Even after thorough researches, there has been no agreement that there is a genetic similarity between the modern human beings and the Neanderthals (Public Library of Science 2010). The proponents of this fact keep on arguing that there are similarities which possibly might have emerged from genetic exchange. However, their rivals claim that very minimal genetic exchange happened. The problems can be resolved by sequencing the Mitochondrial DNA but still the human DNA present in the available fossils is so small to be used effectively (Public Library of Science 2010).
As reported by Public Library of Science (2010), a related problem is that if a Neanderthals fossil gives way to sequences as the modern human-like DNA, those might be discarded as presumed contaminations, regardless of whether they may be endogenous and represent evidence for a close genetic connection or interbreeding between the two groups.
In order to study the relationship that exist between modern humans and the Neanderthals the various difficulties had to be overcome and a conclusion made that four Neanderthal mitochondrion DNA can be distinguished from those of the modern man (Public Library of Science 2010). This gave room for a study to be carried out to determine the genetic relationship between the modern man and the Neandertal man (Public Library of Science 2010)
In order to study the process of interbreeding when the migrating modern man met with the Neanderthals, it is very important that their ancestral settlements and migration patterns (Trinkaus 2007). It is also important to determine the ancestors of the modern European man. The Neanderthals are believed to have occupied a large part of the Mediterranean Europe (Trinkaus 2007). The Neanderthals are also believed to have occupied the southwestern Asia. Through such movement pattern and migration there might have been interaction between the Neanderthals and the modern European human (Trinkaus 2007). This is because at some point the Neanderthals displaced the early modern European man in order to settle.