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The transcription factor binding sites also called as motifs are short, recurring patterns in DNA sequences that are presumed to have a biological function. Identification of the motifs from the promoter region of the genes is an important and unsolved problem specifically in the eukaryotic genomes. In this paper, we present a niched Pareto genetic algorithm to identify the regulatory motifs. This approach is based on the maximization of two objectives of the problem that is the motif length and the consensus similarity score. A long motif means it is less likely to be a false motif. The similarity score represents a motifs probability of conservation in a given set of sequences. Proposed method can find multiple, variable length motifs. In this method, we represented a candidate motif as a combination of length and starting position of the motif in each sequence of the co-regulated genes. This enables the algorithm to identify multiple motifs of variable length. We applied this approach on various data sets and the results show that it can find multiple motifs of variable length in co-regulated genes.