We compute Yukawa couplings in type IIB string theory compactified on a non factorisable six-torus in the presence of D9 branes and fluxes. The setting studied in detail, is obtained by T-dualising an intersecting brane configuration of type IIA theory compactified on a torus generated by the SO(12) root lattice. Particular deformations of such torus are taken into account and provide moduli dependent couplings. Agreement with the type IIA result is found in a non trivial way. The classical type IIB calculation gives also information on a factor accessible only by quantum computations on the type IIA side.
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