A method and system of merging gated-clock domains in a semiconductor design includes producing, for each subset of clock gating functions in an initial set of clock gating functions, a set of quantified functions produced by existentially quantifying each clock gating function in the subset over a set of variables that are not part of the support sets of the other clock gating functions of the subset. If the set of quantified functions are equal, selecting one as a super clock gating function and adding it to the set of super clock gating functions. The set of super clock gating functions are sorted according to a criterion and the best is selected and added to the set of final clock gating functions. The remaining super clock gating functions are modified to prevent flip-flops gated by the selected super clock gating function from being gated by remaining super clock gating functions.