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The main objective of middleware is to shield the details of network and operating systems while facilitate the rapid deployment of applications. In this paper, we discuss the middleware in wireless sensor network and analyze the strengths and weaknesses of mobile agent based middleware, then a new mobile agent based publish/subscribe middleware is proposed, which improves the efficiency of transmitting agent by using the publish/subscribe mechanism to build interest route. Finally, we evaluate its performance compared to the traditional working mechanisms from perspectives of energy consumption and execution time. The demonstrate results show that our proposal is more reliable and flexible as well as multifunctional than many other existed proposals.