The main purpose of this study is to develop an algorithm to solve the scheduling problems of FMS using Petri-net is well suited to model the dynamics of FMS and Petri-net is an ideal tool to formulate scheduling problems with routing flexibility and shared resources. By using the marking of Petri-net, We can model features of discrete even system, such as concurrency, asynchronous, conflict and non-determinism. The proposed algorithm in this paper can handle back-tracking using the marking of Petri-net. The results of the experiment show that marking is one of the best ways that describe exactly movement of the discrete event system. To show the effectiveness of the algorithm suggested here, we compare it with L1 algorithm using the Petri-net through the test on randomly generated test problems.