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In recent years mobile ad-hoc networks have become very popular because of their widespread usage. Cooperation among the nodes in ad-hoc networks is an important issue for communication to be possible. In the literature there are many routing protocol for ad-hoc networks. This paper proposes a routing protocol based on mobile agents which identifies the best possible routes between nodes using reputation. Reputation refers to the opinion of one node as seen by other nodes. The proposed routing protocol uses the reputation mechanism to eliminate malicious nodes. Mobile agent is a software module that moves from host to host in a network and informs the best route to the source node. The simulation results prove that the reputation based routing protocol performs better than existing routing protocols.