Due to the complexity of part flow and limited resources, FMS(Flexible Manufacturing System) develops blocking, starvation and deadlock problems, which reduce its performance. In order to minimize such problems buffers are imposed between workstations of the manufacturing lines. In this paper, we are concerned with finding the optimal buffer allocation with regard to maximizing system throughput in limited total buffer capacity situation of FMS. A dynamic programming algorithm to solve the buffer allocation problem is proposed. Computer simulation using Arena is experimented to show the validation of the proposed algorithm.