Masses of heavy Standard Model (SM) fermions (top-quark, bottom-quark and tau-lepton) play an important role in the analysis of theories beyond the SM. They serve as low-energy input and reduce the parameter space of such theories. In this paper Minimal supersymmetric extension of the SM is considered and two-loop relations between known SM values of fermion masses and running parameters of the MSSM are studied within the effective theory approach. Both b-quark and τ-lepton have the same quantum numbers with respect to SU(2) group and in the MSSM acquire their masses due to interactions with the same Higgs doublet. As a consequence, for large values of tan β parameter corresponding Yukawa couplings also become large and together with tan β can significantly enhance radiative corrections. In the case of b-quark two-loop 
contribution to the relation between running bottom-quark mass in QCD and MSSM is known in literature. This paper is devoted to calculation of the NNLO corrections proportional to Yukawa couplings. For the τ-lepton obtained contribution can be considered as a good approximation to the full two-loop result. For the b-quark numerical analysis given in the paper shows that only the sum of strong and Yukawa corrections can play such a role.
