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The connection between production scheduling and transportation scheduling is getting closer in smart manufacturing system, and both of those problems are summarized as NP-hard problems. However, only a few studies have considered them simultaneously. This paper solves the integrated production and transportation scheduling problem (IPTSP) in hybrid flow shops, which is an extension of the hybrid flow shop scheduling problem (HFSP). In addition to the production scheduling on machines, the transportation scheduling process on automated guided vehicles (AGVs) is considered as another optimization process. In this problem, the transfer tasks of jobs are performed by a certain number of AGVs. To solve it, we make some preparation (including the establishment of task pool, the new solution representation and the new solution evaluation), which can ensure that satisfactory solutions can be found efficiently while appropriately reducing the scale of search space. Then, an effective genetic tabu search algorithm is used to minimize the makespan. Finally, two groups of instances are designed and three types of experiments are conducted to evaluate the performance of the proposed method. The results show that the proposed method is effective to solve the integrated production and transportation scheduling problem.