We study the flavor structure in intersecting D-brane models. We study anomalies of the discrete flavor symmetries. We analyze the Majorana neutrino masses, which can be generated by D-brane instanton effects. It is found that a certain pattern of mass matrix is obtained and the cyclic permutation symmetry remains unbroken. As a result, trimaximal mixing matrix can be realized if Dirac neutrino mass and charged lepton mass matrices are diagonal.
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