The calculation of Yukawa couplings in F-theory GUTs is developed. The method is applied to the top and bottom Yukawa couplings in an SU(5) model of fermion masses based on family symmetries coming from the SU(5)_perp factor in the underlying E(8) theory. The remaining Yukawa couplings involving the light quark generations are determined by the Froggatt Nielsen non-renormalisable terms generated by heavy messenger states. We extend the calculation of Yukawa couplings to include massive states and estimate the full up and down quark mass matrices in the SU(5) model. We discuss the new features of the resulting structure compared to what is usually assumed for Abelian family symmetry models and show how the model can give a realistic quark mass matrix structure. We extend the analysis to the neutrino sector masses and mixing where we find that tri-bi-maximal mixing is readily accommodated. Finally we discuss mechanisms for splitting the degeneracy between the charged leptons and the down quarks and the doublet triplet splitting in the Higgs sector.
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