Evolutionists believe that modern humans have descended from a common ancestor with Neanderthals, who went extinct as modern humans continued to evolve. This view is supported by a recently published phylogenetic tree showing that Neanderthal and Denisovan Y chromosomes are different from all modern Y chromosomes. But this tree is rooted to show that all humans, including Neanderthals, and Denisovans, descend from a common ancestor with chimpanzees. The study presented here uses a reconstruction of this Y chromosome tree based on the biblical assumption that all humans have descended from Noah. The tree, constructed using a proposed 'Noah' root, shows that Neanderthal and Denisovan Y chromosomes descended from Noah's Y chromosome in the line of Ham. The ancient Y chromosomes are compared to moderns by analysis of sequence similarity and shared alleles revealing that, although they differ from most moderns, they are like modern Y chromosomes in the A haplogroup. The long tree branches in this proposed Noah-rooted tree indicate high Y chromosome mutation rates for the Neanderthal, Denisovan, and modern A haplogroup Y chromosomes. The Neanderthal Y chromosome is also compared to other Stone Age Y chromosomes with similar results. Issues discussed include the problems of using ancient DNA, the causes of high mutation rates, the migration of Neanderthal into Europe following the Babel event and the likely causes of Neanderthal extinction. Since Neanderthal Y chromosome lineages may persist in the world, a plan to find these lineages is proposed. The conclusions of this analysis remain tenuous due to the small sample size, just a few Neanderthal Y chromosomes have been sequenced, and the difficulty of using ancient DNA. Yet, understanding the genetics of human history requires that data be interpreted in the light of Genesis, which records that all men have descended from Noah.