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York gum (Eucalyptus loxophleba Benth) is widely planted in semi-arid regions of Australia for the production of Eucalyptus oil, a mixture of terpenes dominated by the monoterpene 1,8-cineole. Increasing oil yield in this species would improve the profitability of this crop and enhance its use in sustainable land management systems in Australia. To this end, we sequenced ten structural genes in the terpene biosynthetic pathway of similar to 400 individuals of E. loxophleba. Of the 4353 allelic variants identified, 1347 had a minor allele frequency >0.01. These were associated with three key traits of essential oil yield (concentration of 1,8-cineole, alpha-pinene and total terpenes). Three variants associated with alpha-pinene, two with 1,8-cineole and eight with total terpenes (13 total). The variants were mostly located in introns of the final three biosynthetic steps of the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway (mcs, hds and hdr). Effect size varied from 2.7 to 6.8%, comparable to similar studies in forest trees. The cumulative effect size of the unlinked variants was 34.8% for total terpenes, although this is likely to be a high estimate. These results provide the basis for the development of molecular breeding methods for improving essential oil yield in this industrially important species.