During 2009–2012, wild animals and their ticks were sampled in two areas within the Amazon biome of Brazil, in the states of Mato Grosso and Pará. Animal tissues, blood, and ticks were molecularly tested for Rickettsia and Coxiella DNA. A total of 182 wild animals were sampled, comprising 28 mammalian, five avian, and three reptilian species. Animal tissues or blood were all negative for Rickettsia or Coxiella DNA. A total of 454 ticks (22 larvae, 226 nymphs, 127 males, 79 females) were collected from 52 (28.6 %) animals, and identified into 15 species: Amblyomma cajennense, A. naponense, A. humerale, A. nodosum, A. goeldii, A. oblongoguttatum, A. longirostre, A. calcaratum, A. coelebs, A. pacae, A. geayii, A. rotundatum, A. auricularium, A. ovale, and Haemaphysalis juxtakochi. While no Coxiella DNA was identified in ticks, six Rickettsia species were detected in the ticks. “Candidatus Rickettsia amblyommii” was the most common agent, detected in four tick species, A. cajennense, A. auricularium, A. longirostre, and A. humerale. The second most common agent, R. bellii, was detected in A. humerale and A. naponense. Rickettsia rhipicephali was detected in H. juxtakochi, and R. felis in A. humerale. Two possible new Rickettsia species were detected in A. naponense ticks, namely, a novel spotted fever group agent close-related to R. africae in Pará, and a novel Canadensis group agent in Mato Grosso. Results of the present study expand our knowledge on the tick fauna, and on the yet infantile knowledge of tick-borne rickettsiae in the Amazon biome.