  We consider the K^0 - \bar K^0 and B^0 - \bar B^0 mixings in the MSSM with
the two-Higgs-doublet scalar sector featuring explicit CP violation, and the
Yukawa sector of type II. In the case of strong mixing between CP-odd and
CP-even states the existence of light charged Higgs is allowed in the model.
The mass splitting \Delta m_{LS} and the amount of indirect CP violation
\epsilon are calculated. In the limit of effective low-energy approximation the
nonstandard effects are shown to be negligibly small in \Delta m_{LS} and
\epsilon for the K^0-mesons, being almost independent on the charged Higgs
boson mass. However, for the B_d^0 - \bar B_d^0 and B_s^0 - \bar B_s^0 systems
the effects of nonstandard physics are shown to be larger, limiting the MSSM
parameter space.
