Tick-borne diseases usually comprise a complex epidemiological and ecological network connecting the vector, pathogen, and a group of host species. Symptoms associated with Lyme disease have been reported in Brazil, but no Borrelia sp. has been definitively related to these events. Here we have identified a B. lonestari/B. theileri-related spirochete DNA in the cattle tick Rhipicephalus (Boophilus) microplus from Brazil. Four hundred R. microplus and 80 Amblyomma cajennense ticks were screened, and only 1 horse-fed R. microplus was infected. A Borrelia sp. 16S rDNA sequence was amplified by polymerase chain reaction (PCR) from the total tick DNA with 99% similarity to B. theileri and B. lonestari. Partial flaB sequence was also obtained, demonstrating 96% similarity to the B. lonestari flagellin gene, and the resultant putative amino acid sequence demonstrated 97% identity to B. lonestari flagellin. Moreover, partial glpQ sequence demonstrated 92% similarity to the B. lonestari gene, with a putative amino acid sequence 90% identical to the B. lonestari glycerophosphodiester phosphodiesterase. Phylogenetic analyses clearly include this Brazilian Borrelia sp., denoted "Borrelia," sp-BR in a group of spirochetes aligned with B. theileri and B. lonestari. Thus, hard tick relapsing fever group spirochetes represent a clade of widespread bacteria and herein we describe the first molecular identification of a Borrelia sp. in South America.