Global climate change is one of the greatest threats to biodiversity, and one of the most pressing challenges within conservation science and management. Thus, one of the emerging objectives within conservation practice is to identify and conserve areas of heightened resilience and/or evolutionary potential. Previous studies assessing the links between past climatic oscillations and contemporary intraspecific genetic variation have found that climatic refugia (i.e. areas that remained habitable through climatic oscillations) are likely to be areas of increased genetic diversity. However, the influence of climatic refugia on genetic diversity is still largely unexplored within the marine environment, especially within a multi-species context. Here, we explore how paleo-climatic changes since the Last Glacial Maximum (LGM; 21 kya) have influenced the genetic diversity of three southern African rocky shore species, namely the Cape urchin (Parechinus angulosus), granular limpet (Scutellastra granularis), and shore crab (Cyclgrapsus punctatus). We also compare areas of past and future climatic stability to identify resilience hotspots for future conservation planning efforts. To identify climatic refugia we conducted species distribution models (SDMs) to the LGM at 1,000 year intervals, using snapshot simulations with mean sea surface temperature and air temperature as predictor variables. We then tested the relationship between climatic stability and sea level variability with patterns of genetic and genomic diversity using generalised linear models. Finally, we projected species distributions into the years 2050 and 2090 to test for multi-species climatic refugia consistent with the hindcasted distributions. The results show complex relationships between climatic variability, species, and molecular markers, but do suggest climatic refugia shared across all species and timeframes. By combining past and future environmental niche modelling and population genetic analyses, we are able to provide a baseline for both the exposure and sensitivity of rocky shore species to climate change.