Identification of Transcription Factor Binding Sites (TFBS) from the upstream region of genes remains a highly important and unsolved problem particularly in higher eukaryotic genomes. In this paper, we propose a novel approach to identify transcription factor binding sites. This approach combines greedy method and genetic algorithm (CGGA) to search conserved segment in the given sequence set. A new greedy method which can efficiently search a local optimal result is proposed. In order to solve the high complexity of this algorithm, we also give an effective improvement for this method. Then, we describe how to combine genetic algorithm with this greedy method to find the more optimal results. Greedy method is combined to the fitness function of the genetic algorithm. We apply this approach on two different TFBS sets and the results show that it can find correct result both effective and efficient, and for CRP binding sites, it get a more accurate result than Gibbs Sampler, AlignACE and MDGA.