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Dealing with irregular domains, graph signal processing (GSP) has attracted much attention especially in brain imaging analysis. Motor imagery tasks are extensively utilized in brain-computer interface (BCI) systems that perform classification using features extracted from Electroencephalogram signals. In this paper, a GSP-based approach is presented for two-class motor imagery tasks classification. The proposed method exploits simultaneous diagonalization of two matrices that quantify the covariance structure of graph spectral representation of data from each class, providing a discriminative subspace where distinctive features are extracted from the data. The performance of the proposed method was evaluated on Dataset IVa from BCI Competition III. Experimental results show that the proposed method outperforms two state-of-the-art alternative methods.