Neither historical climate nor contemporary range fully explain the extant patterns of molecular diversity in marine species.

Aim: Intraspecific diversity is a significant component of adaptive potential, and thus, it is important to identify the evolutionary processes that have and will continue to shape the molecular diversity of natural populations. This study aims to untangle the possible drivers of intraspecific molecular diversity by testing whether patterns of historical climatic stability or contemporary range position correlate with molecular diversity. Location: South African coastline. Taxa: The cape urchin (Parechinus angulosus), common shore crab (Cyclograpsus punctatus) and granular limpet (Scutellastra granularis). Methods: Species distributions were hindcasted to the Last Glacial Maximum to assess the biogeography of the study species. Linear models were built to compare the relationships between historical climatic stability or contemporary distributional ranges with extant genetic (mtDNA) and genomic (SNP) diversity. Results: We found large differences in the historical ranges among species and time periods. Regions of higher habitat stability corresponded to regions of higher molecular diversity, but historical climatic variability was not a predictor of molecular diversity within linear models. Lower genetic diversity values, and higher genetic differentiation, were detected in edge populations, but this was not consistent across marker type or species. Main conclusions: Both historical and contemporary processes are potentially driving patterns of diversity, but a large portion of the variation in molecular diversity remains unexplained. Our findings suggest that marine species within cool‐temperate bioregions in the Southern Hemisphere may have more complex biogeographic and evolutionary histories than terrestrial taxa and/or coastal species within northern, formerly glaciated regions. [ABSTRACT FROM AUTHOR]