The interaction between bacteria and human is still incomplete. With the recent availability of many microbial genomes and human genome, as well as the series of basic local alignment search tool (BLAST) programs, a new perspective to gain insight into the interaction between the bacteria and human is possible. This study is to determine the possibility of existence of sequence identity between the genomes of bacteria and human, and try to explain this phenomenon in term of bacteriophages and other genetic mobile elements. BLAST searches of the genomes of bacteria, bacteriophages, and plasmids against human genome were performed using the resources of the National Center for Biotechnology Information (NCBI). All studied bacteria contain variable numbers of short regions of sequence identity to the genome of human, which ranged from 27 to 84 nt. They were found at multiple sites within the human genome. The short regions of sequence identity existed between the genomes of bacteria and human, and a hypothesis that viruses, especially bacteriophages, might play a significant role in shaping the genomes of bacterial and human, and contribute to the short regions of sequence identity is developed.