Abstract: Widely used in data-driven computer animation, motion capture data exhibits its complexity both spatially and temporally. The indexing and retrieval of motion data is a hard task that is not totally solved. In this paper, we present an efficient motion data indexing and retrieval method based on self-organizing map and Smith-Waterman string similarity metric. Existing motion clips are first used to train a self-organizing map and then indexed by the nodes of the map to get the motion strings. The Smith-Waterman algorithm, a local similarity measure method for string comparison, is used in clustering the motion strings. Then the motion motif of each cluster is extracted for the retrieval of example-based query. As an unsupervised learning approach, our method can cluster motion clips automatically without needing to know their motion types. Experiment results on a dataset of various kinds of motion show that the proposed method not only clusters the motion data accurately but also retrieves appropriate motion data efficiently.