Eucalyptus melliodora, a tree native to eastern Australia, has strong timber and a high nectar load, making it economically important and a vital source of food for nectar-consuming species. In 1993, an individual of the species was discovered that harbors a somatic mutation conferring herbivore resistance to a number of branches on the tree via differential terpenoid production. Transcriptomic analysis has provided limited determination of the genetic source of this variation. We generated whole-genome Illumina sequences for 24 samples from this tree (3 samples from 8 branches), for a total of 700x coverage. We called variants using both a reference-free De-Bruijn variant caller DiscoSNP++ and GATK using the high-quality reference for Eucalyptus grandis, a closely-related species. We find that the phylogeny of the variants identified by both methods reflects the branching pattern of the tree, though the phylogeny is affected by short interior nodes. We also discuss the challenges of estimating phylogenies for somatic tissues. This data presents an opportunity to study the rate and processes of somatic mutations in plants, with connections to cancer and the evolution and maintenance of multicelluarity.