| Summary: | <i>Coxiella burnetii</i>, the zoonotic agent of Q fever, has a worldwide distribution. Despite the vast information about the circulating genotypes in Europe and North America, there is a lack of data regarding <i>C. burnetii</i> strains in South America. Here, we show the presence of novel multispacer sequence typing (MST) genotypes of <i>C. burnetii</i> in two clusters detected in Brazil and Argentina that seem to be distant in parenthood. Argentinian strains isolated from a tick belongs to a new phylogenetic branch of <i>C. burnetii</i>, and the Brazilians strains may be related to MST 20 and 61. Multilocus variable number tandem repeats analysis (MLVA) typing provided a deeper resolution that may be related to host clusters of bovines, caprine, ovine, and ticks. Our results corroborate with the reports of geotypes of <i>C. burnetii.</i> Thus, we highlight the need for more genotyping studies to understand the genetic diversity of <i>C. burnetii</i> in South America and to confirm the hypothesis of host-related genotypes. We also emphasize the importance of virulence studies for a better understanding of Q fever in the region, which may help in surveillance and disease prevention programs.
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