  In this work we study the CP violation for $\bar{B^0}\to J/\psi K_s$ and
$\bar{B^0}\to \phi K_s$ up to leading and next-to-leading order QCD corrections
in the standard model, two-Higgs-doublet model and the minimal supersymmetric
extension of the standard model. We also study the effect of new physics on the
branching ratios of these two decay modes. We find that within the parameter
space constrained by the observation of the decay $b\to s\gamma$, new physics
does not affect the CP asymmetries greatly, and the prediction of new physics
to the branching ratios of $\bar{B^0}\to J/\psi K_s$ and $\bar{B^0}\to \phi
K_s$ is the same as that of the standard model up to a minor discrepancy as far
as the Yukama couplying constants are perturbative.
