In this paper, a gene-handling method for evolutionary algorithms (EAs) is proposed. Such algorithms are characterized by a nonanalytic optimization process when dealing with complex systems as multiple behavioral responses occur in the realization of intelligent tasks. In generic EAs which optimize internal parameters of a given system, evaluation and selection are performed at the chromosome level. When a survived chromosome includes noneffective genes, the solution can be trapped in a local optimum during evolution, which causes an increase in the uncertainty of the results and reduces the quality of the overall system. This phenomenon also results in an unbalanced performance of partial behaviors. To alleviate this problem, a score-based resampling method is proposed, where a score function of a gene is introduced as a criterion of handling genes in each allele. The proposed method was empirically evaluated with various test functions, and the results show its effectiveness.