Resolution of systematic associations and species boundaries is vital for developing conservation priorities for threatened taxa. A complex of Fontainea (Euphorbiaceae) populations, endemic to rainforest communities in central-eastern Australia, comprises several taxonomically challenging species. Fontainea oraria is Critically Endangered, with only one natural population of 10 mature individuals, with the closely related species F. australis being listed as Vulnerable. A recently discovered Fontainea population (currently nominated as F. sp. Coffs Harbour) with taxonomic similarities to F. oraria has been provisionally listed as Critically Endangered, with fewer than 40 individuals. This study employed an integrative approach, combining genetic data and morphometrics to determine species boundaries for three threatened Fontainea population groups as a model system for an integrative approach to delimiting cryptic species. Although our results suggest the potential subdivision of the population groups into three taxa, caution is warranted because this hypothesis remains inconclusive. Taxonomic challenges demand a careful approach, acknowledging the possibility of alternative interpretations. Contrary to supporting distinct species, our morphological and genetic data may also be interpreted as indicative of a single species with geographic variation, a phenomenon observed in genetically linked populations experiencing isolation by distance. Overall, we highlight the need for further research to establish species limits to guide conservation actions.