Ticks are vectors of a variety of pathogens, including Francisella tularensis. Bacteria in the genus Francisella have been identified mostly in the Northern Hemisphere and include tick endosymbionts. Francisella has never been described in Brazil, where Amblyomma spp. ticks are known as the vector of many bacterial zoonotic pathogens. In the present work, we have identified bacterial DNA sequences with identity to Francisella genes in Amblyomma dubitatum Neumann Dermacentor nitens (Neumann), and Rhipicephalus microplus (Canestrini) in Brazil. DNA fragments with homology to Francisella spp. 16S rDNA and the tul4 gene were polymerase chain reaction amplified from tick DNA samples collected in Minas Gerais and Mato Grosso states. These sequences were 96–99% identical to the reported sequences for Franeisella-like tick endosymbionts (FLEs). Sequences similar to the tularemia agent F. tularensis pathogenicity island gene iglC and its regulatory gene mglA also were identified in FLEs.