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Naturally patchy ecosystems are models for other systems currently undergoing anthropogenic habitat fragmentation. Understanding patterns of gene flow in these model systems can help us manage species and ecosystems threatened by human impacts. The mound springs of central Australia represent such a natural model ecosystem, supporting a unique aquatic fauna distributed within an inhospitable arid landscape. Moreover, these springs are being impacted by over extraction of groundwater, providing a unique opportunity to look at dispersal in a patchy habitat that is changing. The present study represents the first fine scale analysis of gene flow under different scenarios of habitat connectivity for the endangered mound spring snail, Fonscochlea accepta. Within a single spring group pairwise estimates of F-ST between springs were very low (ave 0.015) with no association found between genetic distance and a series of geographical distance matrices based on the degree of habitat connectivity among the springs: results implying unstructured dispersal and limited population isolation. However, results from Bayesian assignment tests showed that on average approximately 97% of snails were assigned to their spring of origin. In a preliminary analysis at broader geographic scales (among spring groups) the results from F-ST estimates, Mantel correlation analyses and assignment tests all suggest much stronger and geographically correlated population structuring. While varying results from F-statistics and Bayesian analyses stem from the different information they utilise, together they provide data on contemporary and historical estimates of gene flow and the influence of landscape dynamics on the spatial genetic patterning of the springs.