How is genetic speciation defined?
Speciation in sexually-reproducing organisms can be identified as the inability to produce viable offspring. In other words, when two suspected sub-species are not able to produce viable offspring, they can be considered to be two species. In this case it is not so much determined at the molecular level, but at the organismal level. 

This mating procedure does not work in asexually reproducing species. In this case molecular techniques are needed. Navarro &amp; Barton (2003) investigated what the molecular differences were induced by evolution by comparing the genomes of humans and chimpansees. These two species diverged relatively late in evolution and their DNA differs by about 2.1%. It turned out that the main differences between the two genomes were clustered around regions where chromosomes were rearranged. Although indicative of the cause of speciation, it can nonetheless also be the result of it. We can never be sure. 

Reference
- Navarro &amp; Barton, Science (2003); 300: 321-4