We study wavefunctions on D7-branes with magnetic fluxes in the conifold. Since some supersymmetric embeddings of D-branes on the AdS 5 × T 1,1 geometry are known, we consider one of the embeddings, especially the spacetime filling D7-branes in which (a part of) the standard model is expected to be realized. The explicit form of induced metric on the D7-branes allows us to solve the Laplace and Dirac equations to evaluate matter wavefunctions in extra dimensions analytically. We find that the zeromode wavefunctions can be localized depending on the configuration of magnetic fluxes on D7-branes, and show some phenomenological aspects.