Abundant, exceptionally well-preserved cranial material of the zygomaturine diprotodontid Nimbadon lavarackorum is described from AL90 site, a middle Miocene deposit in the Riversleigh World Heritage Area, Queensland, Australia. The material has enabled a comprehensive assessment of the expected level of morphological variation within a fossil marsupial species from a single locality, thus forming a benchmark for determining species boundaries in extinct marsupials. Variation is assessed by quantitative and qualitative means. Univariate analyses of N. lavarackorum cranial and dental dimensions indicate low coefficients of variation consistent with expected values for single species populations. Conversely, qualitative analyses indicate high levels of morphological variation, particularly in structures previously deemed phylogenetically significant, such as the upper third premolar. Some cranial variation may be due to sexual dimorphism or ontogeny but there appears to be a high degree of intraspecific morphological variation. Features once regarded to distinguish N. whitelawi from the type species fall within the boundaries of that intraspecific variation and N. whitelawi is herein regarded as a junior synonym of N. lavarackorum. Comparison with morphological variation in the Miocene diprotodontid Neohelos stirtoni suggests that N. lavarackorum was a less variable species overall, reflecting differences between the taxa in body size, home range, and habitat preference and stability. Nimbadon lavarackorum was a relatively small (75–120 kg), possibly gregarious browsing species probably restricted to closed-forest habitats.