Trypanosomes and Leishmania are vector-borne parasites associated with high morbidity and mortality. Trypanosoma lewisi, putatively introduced with black rats and fleas, has been implicated in the extinction of two native rodents on Christmas Island (CI) and native trypanosomes are hypothesized to have caused decline in Australian marsupial populations on the mainland. This study investigated the distribution and prevalence of Trypanosoma spp. and Leishmania spp. in two introduced pests (cats and black rats) for three Australian locations. Molecular screening (PCR) on spleen tissue was performed on cats from CI (n = 35), Dirk Hartog Island (DHI; n = 23) and southwest Western Australia (swWA) (n = 58), and black rats from CI only (n = 46). Despite the continued presence of the intermediate and mechanical hosts of T. lewisi, there was no evidence of trypanosome or Leishmania infection in cats or rats from CI. Trypanosomes were not identified in cats from DHI or swWA. These findings suggest T. lewisi is no longer present on CI and endemic Trypanosoma spp. do not infect cats or rats in these locations.