This paper is concerned with the development of optimal algorithms for multi-stage flowshop scheduling problems with sequence dependent setup times. In the previous researches the setup time of a job is considered to be able to begin at the earliest opportunity given a particular sequence at the start of operations. In this paper the setup time of a job is considered to be able to begin only at the completion of that job on the previous machine to reflect the effects of the setup time to the performance measure of sequence dependent setup time flowshop scheduling. The results of the study consist of two areas; first, a general integer programming(IP) model is formulated and a nixed integer linear programming(MILP) model is also formulated by introducing a new binary variable. Second a depth-first branch and bound algorithm is developed. To reduce the computational burdens we use the best heuristic schedule developed by Choi(1989) as the first trial. The experiments for developed algorithm are designed for a 433 factorial design with 360 observations. The experimental factors are PS(ratio of processing time to setup time), M(number of machines), N(number of jobs).