True they are genetically different but that's not the definition of a 'species'. There is a level of politics in biology over what constitutes a species and what does not.
Technically a 'species' is something that interbreeds but does not breed with members outside of it's species and mating produces reproductive offspring. (at least this is the old mayr definition that everyone uses)
The problem is that neanderthals and humans matings produced viable offspring. So is 'neanderthal' a species or not?
The same issue is a problem with the Galapagos finches, which are the holy cows of darwinian genetics. By Mayr's definition they should not be able to interbred and produce viable offspring. However, apparently they can interbreed and therefore are not technically different species.
No one in science want's to badmouth the masters, so Darwin's theory of Galapagos finch species will quietly be put back in the Victorian cabinet while we invent a new 'genetics' based theory of 'species' that makes everyone happy. However, life is not easily classified. Viruses? Species? Bacterial plasmid replication?
There is a lot of politics in the life sciences. Naming a new species or having your name on a species is a big deal. It reminds me of Cope/Marsh and the dinosaur finds (https://en.wikipedia.org/wiki/Bone_Wars) of the early 20th century. They both screwed up the identification of many species so that they could out publish the other and left the mess for future scientists to clean up.
My feelings on this is that we still don't have enough evidence about the genetic makeup of humans to really make any conclusions on anything. Example:
What is the blood type in the reference sequence for the human genome?? We know that there is A, B, A/B and O which represent 4 different genotypes (an AA sequence, a BB sequence, an AB sequence and a missing sequence from both alleles).
If I sequence a neatherthal with blood type A and a human with blood type O, are we genetically divergent?? How can you come to this conclusion unless you know the plasticity of each genome. (i.e. I can't identify a nucleotide change in blood type gene for a type O human because the gene is absent)
It looks like most of the research has been on mtDNA which is passed from mother to child. If we can't find a mtDNA match, it might just mean that there is no maternal linage that can be traced back to that sequenced individual. (i.e. all the children of that mother died out at some point)
Different species? That's a question for politics imho. I personally think that life shuns classification. BTW sorry for the ramble :0