Granite outcrops represent an isolated island habitat and, in ancient landscapes, may harbour species with complex evolutionary histories. Phylogenetic analysis of these species may reveal the influences of evolutionary processes over long time frames. Phylogenetic relationships from chloroplast and nuclear genome analysis were investigated in Eucalyptus caesia, a bird-pollinated mallee endemic to granite outcrops in the South-western Australian Floristic Region. The results obtained revealed high population and haplotype divergence, suggesting restriction to the specific habitat of granite outcrops over long time frames with genetic drift as the most significant evolutionary force. The hypothesis of derivation of ssp. magna from ssp. caesia was not supported by the pattern of diversity in either the chloroplast or the nuclear genome and the two subspecies were not monophyletic. Eucalyptus caesia displays significant clonality yet little evidence of inbreeding depression, suggesting deleterious mutations causing inbreeding depression have been purged. © 2008 Department of Environment and Conservation. Journal compilation © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 177–188.