Mobile Ad hoc Networks (MANETs) are short lived networks that are greatly utilized in many applications such as special outdoor events, for communications in regions having no wireless infrastructure as in natural disasters, military operations, mine site operations and urgent business meetings. The self-organizing properties of its nodes forming the network are rapidly deployable and possess no infrastructure. Hence securing MANETs is a primary concern due to the absence of a central infrastructure and node mobility for which Intrusion Detection System (IDS) has been adopted in addition to the primary lines of defence such as cryptography and authentication. A Hierarchical IDS, namely, the Zone based IDS, functions in MANETs based on node collaboration and detects network layer intrusions with better accuracy. The proposed Cross Layer Detection in cohesion with anomaly detection technique of Zone based IDS aids in detecting attacks originating from the deeper layers of protocol stack, namely, physical and MAC layer thus providing better monitoring and improving the detection accuracy in Zone based IDS. The simulation results showcase an effective increase in detection rates and reduced false positives.