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Clustering algorithms are a common method for data analysis in many science field. They have become popular among biologists because of ease to discovery similar cellular functions in gene expression data. Most approaches consider the gene clustering as an optimization problem, where an ad-hoc cluster quality index is optimized which can be defined regarding gene expression data or biological information. However, these approaches may not be sufficient since they cannot guarantee to generate clusters with similar expression patterns and biological coherence. In this paper, we propose a bi-objective clustering algorithm to discover clusters of genes with high levels of co-expression and biological coherence. Our approach uses a multi-objective evolutionary algorithm (MOEA) that optimizes two index based on gene expression level and biological functional classes. The algorithm is tested on three real-life gene expression datasets. Results show that the proposed model yields gene clusters with higher levels of co-expression and biological coherence than traditional approaches.