The fungal genus Colletotrichum has many plant pathogens which are responsible for substantial losses to many crop species globally. While known for their wide host range in commercial systems, little is known about the diversity of Colletotrichum species associated with Australian native plants. This study aims to improve our understanding of the taxonomic diversity of Colletotrichum species from Australian native plants. A total of 41 Colletotrichum isolates, collected over the past 50 years from Australian native plants, were obtained from state culture collections: VPRI in Victoria and BRIP in Queensland. Although many isolates have been previously identified using morphological characters, species resolution of Colletotrichum spp. infecting native plants has yet to be updated to incorporate molecular phylogenetics. Isolates were identified using multigene phylogenetics, which revealed a diversity of Colletotrichum species across six species complexes. Of particular interest were at least two putative new species discovered on a range of Australian native plants in natural and urban environments. These findings highlight the significant diversity of fungal species isolated from Australian native plants residing within our state culture collections. Furthermore, a diversity of Colletotrichum species beyond agricultural systems has been demonstrated, emphasising the importance of exploring plant pathogen diversity and host range in both agricultural and native systems.