Whole genome sequencing is now widely available and an inexpensive means of providing a wealth of information about an organism’s diversity and evolution, yet genome sequences for many important pathogenic bacteria is limited. As an example, Coxiella burnetii are select agent bacteria pathogenic to humans and livestock that are difficult, slow, and dangerous to culture. As a result, few whole genome sequences are available. Metagenomic sequencing offers a means to produce whole genome sequences, but is severely limited and not cost-effective when the target organism occurs in relatively low frequency. Recently, a method of selective whole genome amplification was developed which permits efficient sequencing of target species. In this study, we successfully amplified C. burnetii from 3 environmental samples where the proportion of host DNA overwhelmed pathogen DNA. Our results show a 33 to 150 fold enrichment of the bacteria and allowed for SNP analyses and placement of these samples on a phylogenetic tree. Such analyses were not possible prior to the selective amplification. The process also demonstrates high fidelity with SNPs matching known C. burnetii strains of similar genotypes. The selective whole genome amplification is a valuable tool for the study of a difficult to culture organism and has the potential to facilitate high-throughput population characterizations as well as targeted epidemiological or forensic investigations.