The myth of the genetic differences between northern and southern Chinese was made popular by Cavalli Sfroza 2 decades ago using limited genetic markers taken from medical literature (genes that were highly selective/responsive to environments).

Later advances, especially in Y-chromsome and mtDNA techniques, which can trace paternal and maternal lineages, and increase of autosomal DNA data sets have shown that the genetic difference between north and south Chinese are miniscule. In fact, the genetic difference between Siberians and Cambodians are even not that much.

All eastern Asians fall into the same randomly assigned cluster based on autosomal DNA:
http://bp2.blogger.com/_Ish7688voT0/RdQ8Id...0215.g002-L.jpg
source: p. 4 of
Low Levels of Genetic Divergence across Geographically and Linguistically Diverse Populations from India
http://genetics.plosjournals.org/archive/1...n.0020215-S.pdf

Some or most of the studies can be found at Dienekes:
http://dienekes.blogspot.com/search/label/Clusters

I'll update with the studies' links and pictures of world clusters (since pictures help) when I have time.

But the point is that for the past decade, all studies (autosomal and Y-chromosome and mtDNA) have grouped east Asians together.

Looks interesting.. care to post more about it.

Btw, I'm just puzzled why northern chinese and southern chinese tends to differ in looks and facial structure. I mean northern chinese tends to look more like Mongolians, which differs from southern chinese looks.

Could there still be some genetic difference or were they offshoots from the same source? I would be please if you can enlighten me more on these anthropological aspects.

Your question is rather broad. Looking different is a matter of degree and does not necessarily prove separate origins, nor does "common origins" mean anything unless we narrow the definition.

Let me answer by going to a more extreme polar contrast.

7-11% of the Thai mtDNA (maternal lineage) seems to be originally belonging to the true aboriginal pygmies of the region who resemble Africans. As agriculture spread from southern China 5,000 years ago, these people were absorbed.

http://z6.invisionfree.com/orient/index.php?showtopic=1124

This is invaluable information ,thanks sir.

I am more incline to believe both northern & southern Han-Chinese have shared paternal ancestors,it's the maternal lineage separateS us in physical looks.

Just my unscientific-based opinion.

I am assuming that better immunity genes get selected... (so is Subsaharan African HLA better for Greek area than European?)

I wonder what about native Indonesians/Malays.

It's a little bit strange to see Han is closer to Japanese than Northern Han (closer to South Chinese minorities like Miao, She, Dai) (because people usually assume Southern Han are more mixed with Southern minorities)

I suppose Siberian to Cambodian difference is even larger..

I think we are all from the same source (out of Africa theory), and our genes just changed slowly over generations.
As long as we are not identical there will be some (of course) differences (though can be very minor).

Maybe North/South Chinese are quite different in female ancestors, but I don't think mtDNA lineages will have anything to do with physical looks (which should be controlled by autosomal DNA).