Signature-based detection is the most widely used technique for Intrusion Detection Systems (IDS). One of the major challenges for signature-based IDS is how to keep up with a 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. In this paper, we propose a dynamic model of two-layer signature-based IDS with unequal database, which can detect imminent threats with very high success rate by automatically creating and using a small efficient database, and at the same time, provide mechanisms to detect all other known threats by using a less efficient complementary database.