Computational Molecular Biology, Bioinformatics and Genomics are the most intriguing sciences to understand the human genome and diseases. These sciences use algorithms to analyze, and predict a hypothesis for the huge collected biological data in gene banks. Sequence alignment is the most important topics in bioinformatics which we are concerned with it in this paper. In comparison of bimolecular sequence (i.e.,DNA, RNA, and protein), regions of sequence similarity indicate functional and structural similarity. As a result, Sequence comparison is the main problem in computational biology, such as evolutionary tree reconstruction, genome analysis, and classification of viruses that belong to specific family of viru+ses. So, it is very important to relate common matched parts between DNA or Protein sequences or to determining ancestors sequences of an offspring before it is used in any process. Due to database was large, parallel smith waterman algorithm (SW) we implemented on Field Programmable Gate Arrays (FPGA) to decrease execution time of algorithm, Which gives significant reduction of execution time and sequential (SW) Execution time by half for two parallel process and decrease the FPGA utilization by 65%.