This study tests the general hypothesis that habitat disruption caused by the release of copper mine wastes in coastal waters has a negative impact on gene flow among populations of the kelp Lessonia nigrescens Bory. Hierarchical sampling was performed within continuous, undisturbed stands and at the northern and southern edges of a 40 km gap caused by mine wastes. Our results, based on RAPD markers, showed a strong genetic structure even in the absence of the disrupting effect of the mine wastes. No pattern of isolation by distance is apparent, however, which indicates that populations are at migration-drift disequilibrium, and suggests that most events of spore recruitment and/or gametophyte fertilization occur within a few metres. On the other hand, some long distance dispersal is likely to occur, which prevents isolation by distance within the spatial scale of 40 km. When comparing continuous stands across the disrupted habitat, an increased genetic differentiation associated with the interruption of the species distribution was observed. A Multiple Correspondence Analysis (MCA) clearly separated the sampling units into 2 groups, each representing a separate stand. Other lines of evidence supporting the idea of genetic disruption came from the mean pairwise differentiation estimates (FST) and from the Analyses of Molecular Variance (AMOVA). Finally, the southern edge of the interruption in the distribution of L. nigrescens showed clear signals of a recent founding event, suggesting that northward recolonisation is currently occurring.