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In this study, a simple genetic model is integrated with an established method from landscape ecology to investigate the effect of habitat geometry and availability on genetic drift. Previous ecological modelling has identified a sharp threshold in habitat availability for species’ persistence, beyond which the species rapidly becomes extinct. This study demonstrates the existence of a similar threshold for fixation time of selectively neutral genotypes by genetic drift, the location of which is determined by habitat shape and spatial correlation of habitat loss. Time to fixation is greater for habitats if they are long and thin rather than square. Despite reductions in population size due to habitat loss, fixation time remains relatively constant until a pre-threshold value, beyond which there is often a substantial increase in time to fixation. Further habitat loss results in the percolation threshold being reached and beyond this point the time to fixation decreases very rapidly. This study reveals a complex relationship between habitat availability, habitat geometry and the process of genetic drift. Possible implications of our results for conservation are discussed. Further work is required to improve our understanding of the interaction between evolutionary, ecological and landscape processes.