This paper presents a new fast multipole boundary element method (FM-BEM) for solving the acoustic transmission problems in 2D periodic media. We divide the periodic media into many fundamental blocks, and then construct the boundary integral equations in the fundamental block. The fast multipole algorithm is proposed for the square and hexagon periodic systems, the convergence of the algorithm is analyzed. We then apply the proposed method to the acoustic transmission problems for liquid phononic crystals and derive the acoustic band gaps of the phononic crystals. By comparing the results with those from plane wave expansion method, we conclude that our method is efficient and accurate.