Monitor lizards (Varanidae) are ecologically important components of the Australian fauna and are abundant in Quaternary fossil deposits like those in Naracoorte Caves (South Australia). However, the narrow range of morphological variation in varanids makes identification of their fossil remains difficult. Here we explore use of geometric morphometrics (GM) to assess fossil affinities of varanid cranial material. Five fossils from Naracoorte's Fossil Chamber (Victoria Fossil Cave), represented by two parietals and three dentaries, were included in the GM analysis. Fossils were compared to the parietals and dentaries of reconstructed X-ray computed tomography specimens belonging to modern species that are currently found in the area: Varanus gouldii, Varanus rosenbergi, and Varanus varius. Both dentaries and parietals belonging to these species were consistently distinguished using GM analytical methods, across a range of sizes from immature to large adults. Our sample of fossils were all unambiguously classified as V. varius. The presence of V. varius during the Middle Pleistocene is consistent with forest and woodland environments reconstructed from previous paleoecology and geochemical research for the region. Our results highlight the potential of modern GM methods in identifying Pleistocene fossil material based on comparisons with modern species. Consequently, our paleoecology interpretations and understanding of relationships between changing environments and species distributions over time are greatly improved, with strong implications for species conservation.