Cyclones and other climate disturbances profoundly affect coastal ecosystems, promoting changes in the benthic communities that require time, sometimes even years, for a complete recovery. In this study we have analysed the morphological and genetic changes occurred in top shell (Gibbula umbilicalis and Phorcus lineatus) assemblages from the Bay of Biscay following explosive cyclogenesis events in 2014. Comparison with previous samples at short (three years before the cyclogenesis) and long (Upper Pleistocene) temporal scales served to better evaluate the extent of change induced by these disturbances in a more global dimension. A significant increase in mean size after the cyclogenesis was found for the two species, suggesting selective sweeping of small individuals weakly adhered to substrata. Loss of haplotype variants at the cytochrome oxidase subunit I gene suggests a population bottleneck, although it was not intense enough to produce significant changes in haplotype frequencies. The high population connectivity and metapopulation structuring of the two species in the area likely help the populations to recover from disturbances. At a wider temporal scale, cyclogenesis effects seemed to compensate the apparent decreasing trends in size for P. lineatus occurred after the Pleistocene-Holocene transition. Considering disturbance regimes for population baselines is recommended when the long-term effects of climate and anthropogenic pressures are evaluated.