Eucalyptus globulus Labill. is native to southeastern Australia and is the most important temperate hardwood plantation species in the world. It consists of four subspecies that are morphologically and geographically distinct but that are linked by morphologically and geographically intermediate populations. The Jeeralang provenance, an intermediate population from southeastern Victoria, is an important source of seed for plantations and genetic material for breeding programs because of its superior growth and wood density. To determine the genetic affinities of this provenance, 154 trees from three subspecies and the Jeeralang provenance were sampled. Analysis of 12 morphological characters verified that the Jeeralang provenance is intermediate between subspecies bicostata (Maiden, Blakely, & J. Simm.) Kirkpatr., globulus and pseudoglobulus (Naudin ex Maiden) Kirkpatr., with individuals having closest affinities to either ssp. globulus or ssp. bicostata. However, eight microsatellite loci showed that the Jeeralang provenance has greater affinities to Victorian ssp. globulus to which it is geographically closest. In contrast, Tasmanian and Victorian ssp. globulus are morphologically similar yet appear to be distinct at the molecular level. This study emphasizes the importance of using traits that are unlikely to be influenced by selection when determining the origin and affinities of populations.