Little is known about the prevalence of blood-borne protozoans in native mammals from the Northern Territory in Australia and their potential contribution to the rapid and broad-scale decline of many species. The present study sought to provide baseline information on the prevalence and genetic diversity of potential pathogenic blood-borne protozoans in native mammals from the Northern Territory in Australia. A total of 221 blood samples from four target mammal species (northern brown bandicoots, common brushtail possums, northern quolls and brush-tailed rabbit-rats) were screened by PCR at the 18S rDNA locus for trypanosomes and piroplasms. Sequencing, phylogenetic analysis and microscopy were also conducted. Overall, 27.6% of the animals were positive for at least one haemoprotozoan species. The prevalence of trypanosomes was 17.6%; of these Trypanosoma vegrandis comprised 13.5%, while the remaining 4.1% were positive for Trypanosoma sp. AP-2011aisolate 64, previously reported in possums from Western Australia. This is the first report of T. vegrandis in northern brown bandicoots and first report of Trypanosoma sp. AP-2011a isolate 64 in possums from the Northern Territory. The prevalence of Babesia sp. and Hepatozoon sp. was 5% respectively and phylogenetic analysis identified a novel Babesia species and two novel Hepatozoon sp species. Further investigation is needed to determine the potential clinical impact of these parasites upon their hosts in the Northern Territory and the role they may play in population decline events.