The identification and characterization of bacterial virulence factors is important for effective treatment of bacterial infections, especially in the case of opportunistic human pathogens like Serratia marcescens. In this study I assess the virulence level of five S. marcescens strains by infecting Drosophila melanogaster, a natural host of the pathogen. I had the genomes of these strains sequenced using high-throughput Illumina-Solexa technology, and compared the whole genomes of a highly virulent S. marcescens strain and a non-virulent one to find genes or regions that were absent in the non-virulent strain. Forty-nine putative virulence genes were identified by sequence homology to genes involved in virulence in other pathogens. These putative virulence genes were located in fourteen genetic regions that were missing in the non-virulent strain. These potential virulence factors may prove to be important in the pathogenicity of Serratia marcescens against a broad spectrum of natural hosts.