This study utilised next generation sequencing methodologies to describe patterns of neutral and adaptive variation for two non-model marine invertebrates along an environmentally homogeneous region, the South African west coast. The study also aimed to compare genome-wide variation between two marker types, mtDNA and SNPs, as well as between two invertebrate species, the Cape urchin (Parechinus angulosus) and the Granular limpet (Scutellastra granularis).