A multivariable fractional order PID controller is designed and to get suitable coefficients for the controller, a genetic algorithm with a new topology to generate a new population is proposed. The three parts of the genetic algorithm such as reproduction, mutation, and crossover are employed and some variations in the methods are fulfilled so that a better performance is gained. The genetic algorithm is applied to design FOPID controllers for a multivariable process and the results are compared with the responses of a H infinity, based multivariable FOPID controller. The simulation responses show that in all cases, the genetic-multivariable FOPID controller has suitable performance, and the output of the system has a smaller error. Also, in the proposed method, variations in one output have a smaller effect on another output which is shown the ability of the proposed method to overcome the interaction in the multivariable processes. (C) 2014 Elsevier Ltd. All rights reserved.