  In the context of Calabi-Yau string models we explore the origin of
characteristic pattern of quark-lepton masses and the CKM matrix. The discrete
$R$-symmetry $Z_K \times Z_2$ is introduced and the $Z_2$ is assigned to the
$R$-parity. The gauge symmetry at the string scale, $SU(6) \times SU(2)_R$, is
broken into the standard model gauge group at a very large intermediate energy
scale. At energies below the intermediate scale down-type quarks and also
leptons are mixed with unobserved heavy states, respectively. On the other
hand, there are no such mixings for up-type quarks. Due to the large mixings
between light states and heavy ones we can derive phenomenologically viable
fermion mass hierarchies and the CKM matrix. Mass spectra for
intermediate-scale matter beyond the MSSM are also determined. Within this
framework proton lifetime is long enough to be consistent with experimental
data. As for the string scale unification of gauge couplings, however,
consistent solutions are not yet found.
