ABSTRACT This paper deals with the formal specification and multi-objective optimization of reconfigurable manufacturing systems (RMSs). RMSs are characterized by their dynamic structure, crucial for responding to functional variations, adjusting production capacity and overcoming operational dysfuntions promptly and cos-effectively. The effective utilization of this dynamic capability depends on thorough study and optimization of RMS configurations. To tackle this challenge, a novel formalism called genetic reconfigurable object nets (Gen-RONs) is introduced. Gen-RONs formalism integrates the modeling, verification and reconfiguration capabilities of reconfigurable object nets with advanced multi-objective techniques from genetic algorithms. Within Gen-RONs, Petri nets serve to: (i) encode RMS configurations, (ii) manage RMS scheduling and (iii) employ graph transformation theory rules as genetic algorithm operators for real-time system reconfiguration. Thus, Gen-RONs formalism provides a robust framework for optimizing RMSs using genetic algorithms. To ensure deadlock-free RMS configurations, Gen-RONs incorporate a binary tree-based technique. Furthermore, Taguchi’s method is employed to fine-tune genetic algorithm parameters. The contribution of this paper is demonstrated through a case study involving an RMS and the widely used genetic algorithm NSGA-II. Significant gains in terms of the number of solutions (i.e. configurations) and the criteria values are achieved.