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Background  Bat trypanosomes are implicated in the evolution of the  T. cruzi  clade, which harbours most African, European and American trypanosomes from bats and other trypanosomes from African, Australian and American terrestrial mammals, including  T. cruzi  and  T. rangeli,  the agents of the American human trypanosomiasis .  The diversity of bat trypanosomes globally is still poorly understood, and the common ancestor, geographical origin, and evolution of species within the  T. cruzi  clade remain largely unresolved.    Methods  Trypanosome sequences were obtained from cultured parasites and from museum archived liver/blood samples of bats captured from Guatemala (Central America) to the Brazilian Atlantic Coast. Phylogenies were inferred using Small Subunit (SSU) rRNA, glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH), and Spliced Leader (SL) RNA genes.    Results  Here, we described  Trypanosoma wauwau  n. sp. from  Pteronotus  bats (Mormoopidae) placed in the  T. cruzi  clade, then supporting the bat-seeding hypothesis whereby the common ancestor of this clade likely was a bat trypanosome.  T. wauwau  was sister to the clade  T.  spp-Neobats from phyllostomid bats forming an assemblage of trypanosome species exclusively of Noctilionoidea Neotropical bats, which was sister to an Australian clade of trypanosomes from indigenous marsupials and rodents, which possibly evolved from a bat trypanosome.  T. wauwau  was found in 26.5 % of the  Pteronotus  bats examined, and phylogeographical analysis evidenced the wide geographical range of this species .  To date, this species was not detected in other bats, including those that were sympatric or shared shelters with  Pteronotus. T. wauwau  did not develop within mammalian cells, and was not infective to Balb/c mice or to triatomine vectors of  T. cruzi  and  T. rangeli .    Conclusions   Trypanosoma wauwau  n. sp. was linked to  Pteronotus  bats. The positioning of the clade  T. wauwau/T. spp-Neobats as the most basal Neotropical bat trypanosomes and closely related to an Australian lineage of trypanosomes provides additional evidence that the  T. cruzi  clade trypanosomes likely evolved from bats, and were dispersed in bats within and between continents from ancient to unexpectedly recent times.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-015-1255-x) contains supplementary material, which is available to authorized users.

parasites and vectors

New insights into the evolution of the Trypanosoma cruzi clade provided by a new trypanosome species tightly linked to Neotropical Pteronotus bats and related to an Australian lineage of trypanosomes