The efficient application and characterization of DNA from pathology, clinical, vector, and animal reservoir samples require molecular assays comparable in sensitivity to current TaqMan, SYBR Green, and nested PCR assays. The feasibility of this approach has already been demonstrated in characterizing Rickettsiain samples from Arizona, California, and Mexico, confirming the identity of a new eschar-associated infection caused by R. rickettsii364D and evaluating C. burnetiiin environmental and clinical samples associated with natural outbreaks. The fundamental problem in applying these methods in forensic situations remains in that it is unknown what portion of the population of these agents in nature is represented by the spectrum of available isolates and samples that have been characterized to date. The generation of genome sequences for additional strains of R. rickettsia, R. prowazekii, and C. burnetiiare needed to further evaluate strain variability and provide novel targets for detecting and differentiating strains and isolates. Current sequencing efforts have shown low genetic variation among the genomes of R. prowazekii, more variability among R. rickettsiistrains, and a high degree of variation among the genomes of C. burnetiiisolates. This may necessitate different strategies for the evaluation of these agents, with the differentiation of strains of a low variability agent such as R. prowazekiipotentially requiring the more sensitive level of SNP assay discrimination. Alternatively, for C. burnetii, the high level of genome variability may simplify the development of assays that provide for differentiation of known strains, but such assays may be unable to differentiate novel strains with unique genome sequences or genomic rearrangements.