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This paper presents a new cluster based routing protocol for Wireless Sensor Networks called Energy Based Clustering Self organizing map (EBCS). This new protocol can cluster sensor nodes based on multiple parameters; their energy level and coordinates, through using Self Organizing Map neural network capability in multi dimensional data clustering. Energy based clustering can form energy balanced clusters in order to better balance energy consumption in whole network which will prolong network lifetime while insuring more network coverage by random and dispersed dying of sensor nodes throughout network space. Simulation results approve the advantages of EBCS over two similar protocols, LEACH and LEA2C in the terms of postponement of first node death and preserving more network coverage. Also a new cost function for election of best Cluster Heads based on multi criteria is presented in which the weights of the criteria are determined using an Analytic Hierarchy Process.