In this paper, we consider a flow shop scheduling problem with bypass consideration for minimizing the sum of earliness and tardiness costs. We propose a new mathematical modeling to formulate this problem. There are several constraints which are involved in our modeling such as the due date of jobs, the job ready times, the earliness and the tardiness cost of jobs, and so on. We apply adapted genetic algorithm based on bypass consideration to solve the problem. The basic parameters of this meta-heuristic are briefly discussed in this paper. Also a computational experiment is conducted to evaluate the performance of the implemented methods. The implemented algorithm can be used to solve large scale flow shop scheduling problem with bypass effectively .