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The work in this paper is motivated by a recently published article in which the authors developed an efficient two-stage genetic algorithm for a comprehensive model of a flexible job-shop scheduling problem (FJSP). In this paper, we extend the application of the algorithm to solve a lot streaming problem in FJSP while at the same time expanding the model to incorporate multiple objectives. The objective function terms included in our current work are the minimization of the (1) makespan, (2) maximum sublot flowtime, (3) total sublot flow time, (4) maximum job flowtime, (5) total job flow time, (6) maximum sublot finish-time separation, (7) total sublot finish-time separation, (8) maximum machine load, (9) total machine load, and (10) maximum machine load difference. Numerical examples are presented to illustrate the greater need for multi-objective optimization in larger problems, the interaction of the various objective function terms, and their relevance in providing better solution quality. The ability of the two-stage genetic algorithm to jointly optimize all the objective function terms is also investigated. The results show that the algorithm can generate initial solutions that are highly improved in all of the objective function terms. It also outperforms the regular genetic algorithm in convergence speed and final solution quality in solving the multi-objective FJSP lot streaming. We also demonstrate that high-performance parallel computation can further improve the performance of the two-stage genetic algorithm. Nevertheless, the sequential two-stage genetic algorithm with a single CPU outperforms the parallel regular genetic algorithm that uses many CPUs, asserting the superiority of the two-stage genetic algorithm in solving the proposed multi-objective FJSP lot streaming.