Intrusion Detection Systems (IDS) based on autonomous agents are important security tools that provide protection to hosts and distributed networks. They can be considered critical systems since they can also be target of attacks. For this reason; An innovative IDS architecture, Laocoonte is proposed, its focus of attention is oriented towards its internal security in order to minimize any attack to the system. Laocoonte is a hierarchical system and it has different levels to perform event correlation, also provides central nodes which perform control functions, it also includes a particular scheme of software watermarking and fingerprinting.