Variation in the qualitative composition of volatile leaf oil was examined in the rare Eucalyptus argutifolia and its widespread congener Eucalyptus obtusiflora. The results revealed that, consistent with the pattern seen with allozymes, E. argutifolia had less variation within populations than E. obtusiflora. Total leaf oil diversity was also significantly lower in the rare species. As found with allozymes, most leaf oil diversity was within populations, but there was also a significant proportion of the variation between populations (25.2% and 27.3% for E. argutifolia and E. obtusiflora, respectively). There were significant associations between phenotypic distance based on leaf oils and geographical distance and between phenotypic and genetic distance across all populations, but these associations were not evident within species. Factors leading to reduced variation in E. argutifolia appear to affect all types of variation, but the relationships between different types of variation within the species are less apparent. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 738–745.