This paper considers a exible assembly job shop scheduling problem with sequence dependent setup times, and its objective is the minimization of makespan, which integrates the process planning and scheduling activities. This is a combinatorial optimization problem with substantially large solution space, suggestingthat it is highly di cult to nd the best solution with the exact search method. In this paper, a particle swarm optimization based algorithm is proposed, which applies a novel solution representation method to t the continuous nature of the algorithm in the discrete modeled problem. Numerical experiments also have been performed to demonstrate the eectiveness of the proposed algorithm.