Parasites of the genus Trypanosoma are microorganisms that display wide morphological, biological and genetic variability. Here we present the first description of an isolate of the genus Trypanosoma naturally infecting the tick Amblyomma brasiliense. The ticks were collected from a specimen of Tayassu pecari (Queixada, white-lipped peccary) from the Itatiaia National Park, Itatiaia, Rio de Janeiro, Brazil. The isolate was characterized by molecular, morphometric and biological analyses. A Trypanosoma culture was isolated from crushed nymphal and adult ticks, propagated in the tick cell line IDE8 and maintained in L15B culture medium, incubated at 32 °C. The isolate grew well in L15B medium at 30, 32 and 34 °C but not at lower or higher temperatures. The culture remained stable in axenic L15B medium at 30 °C. Cryopreserved cultures retained viability after cryopreservation in liquid nitrogen. Growth in axenic medium and developmental forms of the trypanosomes were analysed. Analysis of the 18S rDNA region confirmed the authenticity of this new species and the nucleotide sequence was deposited in Genbank. The species was named Trypanosoma amblyommi sp. nov. strain C1RJ. Characteristics related to pathogenicity, involvement with vertebrate hosts, epidemiology, developmental cycle and transmission mechanisms are still unknown. Therefore, further studies are necessary to understand the aspects of the biological cycle of T. amblyommi sp. nov.