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In this paper, a new approach is introduced to reduce the complexity of the Smith Waterman algorithm for FPGA implementation. We have developed the technique for the fastest comparison of the two DNA sequencing using Verilog on the Xilinx ISE 7.1. The Simulation has been running on the ModelSim XE III 6.0. The combinational delay for the proposed smith waterman algorithm based on divide and conquers technique sequencing is 10.214 ns while the original is 10.295 ns. We have proved that smith waterman algorithm based on divide and conquers technique gives better performance than existing technique.