Trypanosoma spp. are protozoan parasites responsible for a number of important diseases worldwide, although they remain understudied in Australia. High-throughput molecular (NGS) and microscopy (confocal, TEM, SEM, FIB-SEM) techniques combined with In vitro research were used to investigate the diversity and biology of avian and marsupial trypanosomas. A number of novel genotypes were characterised (genetically and morphologically) including a novel species in the Trypanosoma cruzi clade (Trypanosoma noyest). Trypanosoma copemani host-parasite interactions were investigated in vitro and exposure to T. copemani was detrimental to cell health. Future research should focus on understanding the role Australian trypanosomas play in their communities.