The dugong (Dugong dugon) is a marine herbivore that inhabits shallow tropical and sub-tropical coastal waters extending from east Africa to Vanuatu, with Australia considered a stronghold of the species. Within Australia, recent mitochondrial DNA analysis identified one lineage that is widespread across the Australian dugong range and one lineage predominately restricted to the east coast of Queensland. In contrast, nuclear data showed fine-scale population sub-structuring within south-east Queensland. This study aimed to examine the degree of population structuring and connectivity of dugongs along the Queensland coast. Analysis using nuclear markers (24 microsatellite loci, n=168 skin samples) identified two genetic clusters within the Queensland population, with an abrupt break over a short geographic distance identified in the Whitsunday Islands region. This genetic break was not apparent in the mitochondrial data (partial control region sequences, n=208 skin samples), which found agreement with the lineages described in the Australia-wide mtDNA study. The cause of the restricted gene flow in the Whitsundays region will be discussed. The outcomes of this study can be used to inform better management of dugongs in the central Queensland/Great Barrier Reef region.