The overall aim of this project was to consider several freshwater invertebrates that are restricted both geographically and climatically to determine their population genetic structure, population distribution and population viability. The study was set in a framework of genetic analysis as genetics can be used to answer a whole suite of conservation focused questions. Specifically, the study concentrated on the population dynamics of three freshwater crayfish from the genus Euastacus: E. hystricosus, E. urospinosus and E. robertsi. Also, in this study I explored the role of two commensal flatworms as proxy species, to aid in disentangling the population structure of their crayfish hosts. These flatworms were Temnosewellia batiola, which is specific to E. hystricosus and Temnosewellia albata, which is specific to E. robertsi. As part of this study, the known distribution of E. urospinosus was increased from 200 km2 to 1225 km2 in area with 26 locations being identified in the Brisbane and Mary River catchments of SE Queensland, Australia (Hurry et al. 2015 Chapter three). Calculations that were undertaken after publication with the ALA (2015) online tool have now calculated an area of occupancy of approximately 76 km2 or an extent of occurrence of 610 km2. Further, mitochondrial DNA sequence data were then used to investigate the population structure and the phylogeographic divergence between four uplands. There was significant population differentiation for the species which conforms to the headwater model of genetic structure. Fragmentation between these uplands was found to be historical as the first divergence between lineages was dated at ~2.1 million years ago (mya).