We discuss a five-dimensional Minimal Supersymmetric Standard Model compactified on a $S^1/Z_2$ orbifold, looking at, in particular, the one-loop evolution equations of the Yukawa couplings for the quark sector and various flavor observables. Different possibilities for the matter fields are discussed, that is, where they are in the bulk or localised to the brane. The two possibilities give rise to quite different behaviours. By studying the implications of the evolution with the renormalisation group of the Yukawa couplings and of the flavor observables we find that, for a theory that is valid up to the unification scale, the case where fields are localised to the brane, with a large $\tan\beta$, would be more easily distinguishable from other scenarios.