In recent years, autonomous mobile robots (AMR) have emerged as a means of transportation system in warehouses. The complexity of the transport tasks requires efficient high-level control, i.e. planning and scheduling of the tasks as well as low-level motion control of the robots. Hence, an efficient coordination between robots is needed to achieve flexibility, robustness and scalability of the transportation system. In this chapter, we present a methodology to achieve coordination in different control layers, namely high-level and low-level coordination. We investigate how the coordination strategies perform in an automated warehouse. We use simulation results to analyse the system performance. We take into account typical performance indicators for a warehouse, such as time to accomplish the transportation tasks and total cost of the system. In addition to the simulation results, we conduct experiments in a small-scale representation of the warehouse.