Climate change pressures species to adapt to shifting environmental conditions. Assessing the genomic basis of local adaptation is essential to anticipate species persistence. Pooled RAD-Seq (ezRAD Pool-Seq) data from the shore crab Cyclograpsus punctatus, the Cape urchin Parechinus angulosus, and the granular limpet Scutellastra granularis collected at six sites across the west, south and east coast were utilised to determine gene regions (SNPs) putatively under selection. Contrasting temperatures between the South African west, south and east coast strongly motivated the experimental investigation of regional differences between populations.