DNA sequence retrieval is a very important topic in bioinformatics algorithm development. However, this task usually spends much computational time to search on large DNA sequence database. In this paper, an efficient hierarchical method is proposed to improve the search speed while the accuracy is being kept constant. For a given query sequence, firstly, a fast local search method using histogram features is used as a filtering mechanism before scanning the sequences in the database. A large number of DNA sequences with low similarity will be excluded for latter searching. The Smith-Waterman algorithm is then applied to each remainder sequences. Experimental results using GenBank sequence data show the proposed method combining histogram information and Smith-Waterman algorithm is a more efficient algorithm for DNA sequence retrieval.