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Identification of structural and sequence motifs in genomic sequences is gaining much attention now a days. Ribonucleic acid or RNA is one of the important biomolecule whose secondary structure defines its functionality. Soft computing techniques like genetic programming have been used for motif identification. In this paper, we propose a method for identifying common structural motifs in a set of RNA sequences by particle swarm optimization technique. The common motif identification finds its application in drug design. To prove the correctness of our approach, we tested it on data sets previously used to find common structural motif using genetic programming approaches. Several experiments were conducted using Signal Recognition Particle (SRP), Ferritin Iron Response Element (IRE) and microRNA sequences. Our results are comparable to the latest genetic programming approach. Some of the results indicate that our method out performs to most of the genetic programming approaches.