In this paper, a machine loading problem in a flexible manufacturing system (FMS) is discussed, with bi-criterion objectives of minimising system imbalance and maximising system throughput in the occurrence of technological constraints such as available machining time and tool slots. A mathematical model is used to select machines, assign operations and the required tools in order to minimise the system's imbalance while maximising the throughput. An efficient evolutionary algorithm by hybridising the genetic algorithm (GA) and simulated annealing (SA) algorithm called GASA is proposed in this paper. The performance of the GASA is tested by using 10 sample dataset and the results are compared with the heuristics reported in the literature. The influence of genetic operators on the evolutionary search in GASA is studied and reported. Two machine selection heuristics are proposed and their influence on the quality of the solution is also studied. Extensive computational experiments have been carried out to evaluate the performance of the proposed evolutionary heuristics and the results are presented in tables and figures. The results clearly support the better performance of GASA over the algorithms reported in the literature.