  We examine the structure of the Yukawa couplings in the 11 dimensional
Horava-Witten M-theory based on non-standard embeddings. We find that the CKM
and quark mass hierarchies can be explained in M Theory without introducing
undue fine tuning. A phenomenological example is presented satisfying all CKM
and quark mass data requiring the 5-branes cluster near the second orbifold
plane, and that the instanton charges of the physical orbifold plane vanish.
The latter condition is explicitly realized on a Calabi-Yau manifold with del
Pezzo base dP_7.
