Selection against inbred progeny is a well-documented phenomenon in natural and experimental populations of trees with mixed mating systems. This inbreeding depression can be expressed at multiple life stages, including early seedling development. Eucalyptus caesia, a long-lived tree that is endemic to granite outcrops in south-west Australia, has an anciently fragmented population structure, low levels of heterozygosity and limited genetic interconnection between stands and small population sizes. To test whether purging of genetic load may have facilitated the persistence of E. caesia on its granite rock habitat, we assessed the early growth and survivorship of seedlings in a common garden trial. A total of 120 seedlings from eight maternal trees were planted in four plots at the study site. Seedling growth rate and survivorship were assessed over 26 months against familial background and level of individual heterozygosity. We found no significant variation in the early growth or survivorship of selfed or outcrossed seedlings, or between seedlings with low or high levels of individual heterozygosity. These results support the hypothesis that purging of genetic load may have reduced the negative impacts of inbreeding in seedlings of E. caesia.