This paper deals with a reentrant hybrid flow shop problem with sequence-dependent setup time and limited buffers where there are multiple unrelated parallel machines at each stage. A mathematical model with the minimization of total weighted completion time is constructed for this problem. Considering the complexity of the problem at hand, an effective cooperative adaptive genetic algorithm (CAGA) is proposed. In the algorithm, a dual chain coding scheme and a staged-hierarchical decoding approach are, respectively, designed to encode and decode each solution. Six dispatch heuristics and a dynamic adjustment method are introduced to define initial population. To balance the exploration and exploitation abilities, three effective operations are implemented: (1) two new crossover and mutation operators with collaborative mechanism are imposed on genetic algorithm; (2) an adaptive adjustment strategy is introduced to re-optimize better solutions after mutation operations, where ant colony search algorithm and modified greedy heuristic are intelligently switched; (3) a reset strategy with dynamic variable step strategy is embedded to re-generate some non-improved solutions. A Taguchi method of design of experiment is adopted to calibrate the parameter values in the presented algorithm. Comparison experiments are executed on test instances with different scale problems. Computational results show that the proposed CAGA is more effective and efficient than several well-known algorithms in solving the studied problem.