In this paper, the flow shop with blocking and sequence and machine dependent setup time problem aiming to minimize the makespan is studied. Two mixed-integer programming models are proposed (TNZBS1 and TNZBS2) and two other mixed-integer programming models, originally proposed for the no setup problem, are adapted to the problem. Furthermore, an Iterated Greedy algorithm is proposed for the problem. The permutation flow shop with blocking and sequence and machine dependent setup time is an underexplored problem and the authors did not find the use of mixed-integer programming models for the problem in any other work. To compare the models, a database of 80 problems was generated, which vary in number of machines and jobs. For the small sized problems, the adapted MILP model obtained the best results. However, for bigger problems, both proposed MILP models obtained significantly better results compared to the adapted models, proving the efficiency of the new models. When comparing the Iterated Greedy algorithm with the MILP models, the former outperformed the latter.