Habitat fragmentation is affecting greater numbers of species as human land use requirements increase. Melaleuca irbyana R.T.Baker (Myrtaceae) is an endangered tea tree which dominates critically endangered, south-east Queensland swamp tea tree forest. It is restricted to isolated populations in south-east Queensland. New disjunct populations have recently been found adjacent to gas pipeline developments in the Brigalow Belt in central Queensland. A population genetics study was undertaken on the species to investigate its diversity to advise conservation and restoration. Primers for microsatellite markers were developed and used to provide the genetic information for the study. M. irbyana was found to possess moderate levels of genetic diversity within populations but this was not correlated with patch size or isolation. However, inbreeding levels were moderately high in all populations, suggesting individuals may be self-fertilised as there was no evidence of clonality detected in this species despite evidence of resprouting. The disjunct populations in central Queensland were genetically distinct, which highlights their importance for conservation of the species. The northern NSW populations are potentially at risk as they are depauperate and genetically distinct. There is differentiation among populations between the geographic regions so care should be taken to consider local provenance in restoration plantings.