The pivotal role of amphibians in food webs and their value as indicators of disequilibrium in ecosystem health have long been recognized by wildlife biologists. However, massive pathogen-induced declines in global amphibian populations reported during the last 30 years served to alert the scientific community that knowledge of amphibian disease ecology, including parasitic and vector-borne conditions, was and remains incipient. Herein, we report the detection of a Rickettsia bacterium infecting larvae of the argasid tick Ornithodoros faccinii, collected from the toad Rhinella ornata, in Southeastern Brazil. Fragments of the genes 16S rDNA, gltA, htrA, sca1, sca4, and ompB were amplified by polymerase chain reaction (PCR), but the sequence encoding the ompA antigen was not detected. Nucleotide sequencing and multi-locus (gltA, htrA, sca1, and sca4) phylogenetic analyses characterized the bacterium, designated Rickettsia sp. strain Itinguçú, as a novel member of the spotted fever group (SFG) of the Rickettsia, closely related to the Rickettsia massiliae and to a lesser extent the Rickettsia helvetica subgroups. The apparent absence of the ompA protein together with limited levels of nucleotide (90.5 %) and amino acid (82–83 %) sequence identity, relative to the ompB gene of other species in the R. massiliae subgroup, were unusual features that may reflect adaptation to selective pressures exerted by the tick and/or amphibian immune systems. The ompB sequence was exploited to develop a low-cost method for differential identification of Rickettsia sp. strain Itinguçú, based on restriction fragment length polymorphism analysis of amplicons (PCR-RFLP). The characterization of this novel bacterium provided an unprecedented record of infection by an SFG Rickettsia in a member of the family Argasidae infesting a cold-blooded animal and raised the number of tick-associated Rickettsia reported in Brazil to sixteen. Moreover, it highlighted the value of and the requirement for continued and extended surveillance of wildlife as potential sources of emerging tick-borne pathogens.