Unitarity constraints for Yukawa couplings are considered in the Two Higgs Doublet Model type III, by using a general expansion in partial waves for fermionic scattering processes. Constraints over general Flavor Changing Neutral Currents are found from that systematic, such bounds compete with those coming from Lagrangian perturbativity requirement but are weaker than those imposed from phenomenological processes and precision tests. Nevertheless, for bounds based on unitarity the number of assumptions is the lowest among phenomenological and theoretical limits. Indeed, these new theoretical constraints are independent of scalar masses or mixing angles for this extended Higgs sector, making them less model dependent.