  A phenomenological analysis of the general two Higgs doublet model is
presented. Possible constraints of the Yukawa couplings are obtained from the
$K^0-\bar{K}^0, B^0-\bar{B}^0$ and $D^0-\bar{D}^0$ mixings. A much larger
$D^0-\bar{D}^0$ mixing than the standard model prediction is possible. It is
shown that the emerging of various new sources of CP violation in the model
could strongly affect the determination of the unitarity triangle. It can be
helpful to look for a signal of new physics by comparing the extracted angle
$\beta$ from two different ways, such as from the process $B\to J/\psi K_{S}$
and from fitting the quantities $|V_{ub}|, \Delta m_{B}$ and $\epsilon$.
