During the normal cycle of transfer between its vector (the flea) and a mammalian host, Yersinia pestis (Y. pestis) is exposed to significantly different environmental conditions. Studies have shown gene expression patterns in Y. pestis differ significantly under these separate conditions. In many bacteria, large-scale gene expression changes are modulated by DNA methylation. To date, methylation patterns of the Y. pestis genome have not been examined. In this study, the methylome of Y. pestis was characterized and whether a change in methylation accounts for change in gene expression was determined. The methylation pattern of the Y. pestis genome, having been characterized, provides a reference methylome. A comparison of the methylation state at different temperatures selected to represent vector and host conditions, showed no significant change in methylation pattern. It is concluded from this study that the methylation pattern of the Y. pestis genome is not altered according to the temperature of its vector or mammalian host.