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In mobile ad hoc networks (MANET) specific Intrusion Detection Systems (IDSs) are needed to safeguard them since traditional intrusion prevention techniques are not sufficient in the protection of MANET. In this paper we present an intrusion detection engine based on neural networks combined with a protection method, which is based on watermarking techniques. We exploit the advantages of information visualization and machine learning techniques in order to achieve intrusion detection. Then, we authenticate the maps produced by the application of the intelligent techniques using a novel combined watermarking embedded method. The performance of the proposed model is evaluated under different traffic conditions, mobility patterns and visualization metrics, showing its high efficiency.