In this paper, the issues of the quark mass hierarchies and the Cabbibo Kobayashi Maskawa mixing are analyzed in a class of intersecting D-brane configurations with Standard Model gauge symmetry. The relevant mass matrices are constructed taking into account the constraints imposed by extra abelian symmetries and anomaly cancelation conditions. Possible mass generating mechanisms including perturbative as well as non-perturbative effects are discussed and specific patterns of mass textures are found characterized by the hierarchies of the scales where the various sources contribute. It is argued that the Cholesky decomposition of the mass matrices is the most appropriate way to determine the properties of these fermion mass patterns, while the associated triangular mass matrix form provides a unified description of all phenomenologically equivalent symmetric and non-symmetric mass matrices. An elegant analytic formula is derived for the Cholesky triangular form of the mass matrices where the entries are given as simple functions of the mass eigenstates and the diagonalizing transformation entries. Finally, motivated by the possibility of vanishing zero Yukawa mass entries in several D-brane and F-theory constructions due to the geometry of the internal space, we analyse in detail all possible texture-zeroes mass matrices within the proposed new context. These new texture-zeroes are compared to those existing in the literature while D-brane inspired cases are worked out in detail.
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