Effective management of species is paramount to their survival in the face of ever-increasing threats. To ensure appropriate conservation management, ongoing monitoring of a species’ dispersal patterns is required to assess the impact potential barriers can have on limiting the exchange of genetic material between populations. Additionally, threats to the overall health of species need to be identified to ensure conservation initiatives are effective. In this thesis, I used an array of genetic techniques to assess the impact of coastal threats to dugongs (Dugong dugong) along the Queensland, Australia coast in an effort to inform conservation management of the Queensland population. The dugong is a long-lived marine mammal that inhabits shallow sub-tropical and tropical coastal waters of the Indo-West Pacific region, feeding on meadows of seagrass. Australia is considered a stronghold for the species due to the large populations still found within its waters, although in Queensland, they are exposed to a number of threatening factors that have potentially contributed to observed population declines.For my first study, I used microsatellite and mitochondrial DNA (mtDNA) genetic markers to investigate the genetic diversity and population structure of dugong populations along the eastern coastline of Queensland, between Torres Strait and Moreton Bay. A seascape genetics approach evaluated the factors that may have influenced dugong dispersal. The microsatellite analysis identified an abrupt genetic break within the Queensland dugong population in the Whitsunday Islands region, with a northern and southern cluster identified. Additionally, Fst values from the mtDNA analysis supported the division of these two clusters. While sea surface temperature and seagrass distribution were not found to be significant factors influencing dugong population structure and genetic distance, an oceanographic phenomenon known as the ‘sticky water’ effect, which is associated with strong tidal currents, may potentially be influencing dugong dispersal.Next, I developed single nucleotide polymorphism (SNP) markers using the double-digest RAD-Seq method to better define Queensland dugong population structure and to identify highly discriminatory, genome-wide genetic markers. After filtering, a dataset of 10,690 loci detected the same abrupt genetic break as in the first study. However, the analysis also indicated a third genetic cluster, suggesting dugong dispersal may have occurred more often across the Whitsundays Islands region than the microsatellite and mtDNA analyses indicated. The identification of genome-wide genetic markers, including a subset of 464 highly differentiating SNPs, provides opportunities for future genomic studies of dugongs.My third study aimed to test the effectiveness of a novel method, the commensal bacterial network, to detect dugong contemporary movements. This method aimed to build a network demonstrating dugong groupings based on whether bacterial genotypes were shared, assuming the transfer of bacteria through either direct or indirect contact among dugongs. Faecal samples were collected and commensal bacterial species cultured and sequenced to determine bacterial genotypes for construction of a network. There was a surprisingly low rate of Escherichia coli culture (n=1, previously used commensal species). A 16S sequencing method identified Staphylococcus warneri as a potentially more suitable species, although low culture success and limited genetic diversity meant it was not possible to build a comprehensive commensal bacterial network to infer dugong contemporary movements.Characterisation and investigation of differences in the dugong faecal microbiome along the Queensland coast was the aim of my fourth study. Diversity profiling demonstrated that the faecal microbial composition of three southern Queensland populations (Clairview, Hervey Bay and Moreton Bay) were different to those of the more northern locations according to Principal Coordinate Analysis and relative abundance averages of the three main phyla, potentially due to differences in diet. Interestingly, the microbiome geographical divide did not align with the genetic divide, potentially indicating ranging movements across the genetic break. Additionally, core microbial families were identified throughout all locations, including Clostridiaceae_1, Lachnospiraceae, Peptostreptococcaceae, Ruminococcaceae, Bacteroidaceae and Flavobacteriaceae, with these possibly important for seagrass digestion.In my final study, antibiotic resistance profiles of bacterial isolates cultured from dugong faecal samples (n=9) collected at two locations, Moreton Bay (urban) and Newry Region (rural), were investigated. Whole Genome Sequencing (WGS) was used to identify resistance and virulence genes. All S. warneri isolates were resistant to penicillin, with two S. warneri isolates displaying multidrug resistance, while E.coli isolates were all resistant to ampicillin. Together with the finding of resistance genes in some of the WGS, these preliminary findings suggest possible contamination of the dugong’s environment with antibiotics from human and agricultural wastewater or run-off.Overall, my findings indicated dugong dispersal is limited across the genetic break, although relatively unrestricted along the remainder of the Queensland coast, with sufficient gene flow to reduce the likelihood of inbreeding and other deleterious effects of low genetic diversity within the two identified clusters. The results from this thesis have the potential to improve dugong conservation management along the urbanised Queensland coast, with maintenance of movement corridors paramount to ensure genetic connectivity.