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To solve the problems in knowledge management system (KMS), such as information sharing, the ability to extend and re-engineer, and the reusable ability of legacy systems in distributed and heterogeneous environments. This article presents a method based on agent and ontology of designing KMS. This method consists of two agencies. One is knowledge agency with three agents supporting knowledge management process. The other is application agency with three agents supporting knowledge application. In this method, ontology is used to represent the knowledge in knowledge base and the content in the message exchanged among agents. To demonstrate the advantages of this method, experiments have been carried out and the results imply that this method is efficient and effective for small and medium-size enterprises to design KMS.