The modern trends in bioinformatics are focused to improve the sophisticated solution to the medical industries. The human society has more impact from the diseases found and they highly reflect from the side of DNA. Any human disease and the person who affect from any disease is based on their DNA sequence. Not only that there are number of biological information can be used to perform any analysis on the disease. The biological information has wide range of applications and can be used for any purpose. In general the biometrics is larger in size and to perform any validation of such wide dimensional features, there require efficient fast applications. We propose an FPGA based multilevel sequence similarity identification to reduce the computational overhead, time and data complexity, GENIE, UNI, dbGap are the benchmarked database considered for the validation of the proposed method. Performance of the proposed method is compared with existing Bloom filter, PSR, SRA and DFT.