Background The subgenus Megatrypanum comprises trypanosomes of cervids and bovids from around the world. Here, Odocoileus virginianus (white-tailed deer = WTD) and its ectoparasite, the deer ked Lipoptena mazamae (hippoboscid fly), were surveyed for trypanosomes in Venezuela. Results Haemoculturing unveiled 20% infected WTD, while 47% (7/15) of blood samples and 38% (11/29) of ked guts tested positive for the Megatrypanum- specific TthCATL-PCR. CATL and SSU rRNA sequences uncovered a single species of trypanosome. Phylogeny based on SSU rRNA and gGAPDH sequences tightly cluster WTD trypanosomes from Venezuela and the USA, which were strongly supported as geographical variants of the herein described Trypanosoma ( Megatrypanum ) perronei sp. n. In our analyses, T. perronei was closest to T . sp. D30 of fallow deer (Germany), both nested into TthII alongside other trypanosomes of cervids (North American elks and European fallow, red and sika deer), and bovids (cattle, antelopes and sheep). Insights into T. perronei life cycle were obtained from early haemocultures of deer blood and co-culture with mammalian and insect cells showing flagellates resembling Megatrypanum trypanosomes previously reported in deer blood, and deer ked guts. For the first time, a trypanosome from a cervid was cultured and phylogenetically and morphologically (light and electron microscopy) characterised. Conclusions In the analyses based on SSU rRNA, gGAPDH, CATL and ITS rDNA sequences, neither cervids nor bovids trypanosomes were monophyletic but intertwined within TthI and TthII major phylogenetic lineages. One host species can harbour more than one species/genotype of trypanosomes, but each trypanosome species/genotype was found in a single host species or in phylogenetically related hosts. Molecular evidence that L. mazamae may transmit T. perronei suggests important evolutionary constraints making tight the tripartite T. perronei –WTD–deer ked association. In a plausible evolutionary scenario, T. perronei entered South America with North American WTD at the Pliocene–Pleistocene boundary following the closure of the Panama Isthmus.