The problem with using genes to define species is that you have to decide a priori that some % divergence defines a species, rather than reproductive isolation (which will give rise to distinct morphologies). It is entirely unclear what % that should be and there is no natural cutoff. Genes are nice because they can resolve lineage relationships well, but assigning a rank to those relationships isn't any easier with genetic data than with morphological data.
Can-o-worms 
Vinny
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“There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that whilst this planet has gone on cycling according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.” -C. Darwin, 1859
