The Internet and computer networks are exposed to an increasing number of security threats. With new types of attacks appearing continually, developing flexible and adaptive security oriented approaches is a severe challenge. Intrusions detection systems (IDSs) are systems that try to detect attacks as they occur or after the attacks took place. IDSs collect network traffic information from some point on the network or computer system and then use this information to secure the network. In this context, signature-based network intrusion detection techniques are a valuable technology to protect target systems and networks against malicious activities. Signature-based detection is the most extensively used threat detection technique for (IDSs). One of the foremost challenges for signature-based IDSs is how to keep up with large volume of incoming traffic when each packet needs to be compared with every signature in the database. When an IDS cannot keep up with the traffic flood, all it can do is to drop packets, therefore, may miss potential attacks. This paper proposes a new model called Signature-based Multi-Layer IDS using mobile agents, which can detect imminent threats with extremely high success rate by dynamically and automatically creating and using small and efficient multiple databases, and at the same time, provide mechanism to update these small signature databases at regular intervals using mobile agents.