With the increasing customization of products there was a need to create new manufacturing systems that were able to satisfy these needs of the market. The Reconfigurable Manufacturing System (RMS) emerges as a more recent approach allowing the reconfiguration of the line and all the manufacturing systems. The balancing line is a common problem in the system reconfiguration but may not be enough, being also important to reconfigure the material handling system itself. Genetic Algorithms (GA) are one of the most known and used alternatives in optimization problems being widely used in shortest path problems like the travelling salesman. In this paper a solution that allows reconfiguring an agent based material handling system using a genetic algorithm is presented.