Cotton (Gossypium hirsutum L.) is grown globally and of significant economic value. Polyploids of several G. hirsutum have been sequenced. Bacteria transmitted by piercing-sucking pests of cotton bolls can cause major yield losses due to resulting seed and lint necrosis. We recovered Serratia marcescens bacterial representatives from rotted bolls fed upon by verde plant bugs (Creontiades signatus) in Texas that is a major US cotton producing state. Here, we present a draft whole genome sequence generated using high-throughput sequencing technology of a S. marcescens strain called CC118 that is capable of causing a comparable cotton boll infection. A focus of the project was to mine for virulence genes and respective host avirluence genes from published cotton genomes. A chromosome (4.4 Mb) and plasmid DNA (>100 kb) were identified. Bacterial genome annotation revealed homologies with pathogenicity determinants including a type IV secretion system and invasins that are known to be involved in the infection process of other pathogens. Further, putative avirulence genes in the allotetrapliod G. hirsutum acc. TM-1 have been potentially identified. This work assists in developing techniques to minimize damages associated with S. marcescens infections.