The task of transcription factor binding sites discovery from the upstream region of gene, without any prior knowledge of what look likes, is very challenging. In this paper we propose an algorithm based on Particle Swarm Optimization (PSO) to identify motif instances in multiple biological sequences. The experimental results on yeast sacchoromyces Cerevisae transcription factor binding sites, demonstrate that the proposed method is working analogous to YMF, MEME and AlignACE algorithms.