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Biogeographic and phylogeographic patterns of sandy beach species are poorly understood, although these ecosystems are heavily impacted by anthropogenic pressures and are of elevated conservation concern. To contribute towards filling the knowledge gap on sandy beaches, we made use of phylogeographic approaches to determine levels of genetic structuring and diversity for Tylos granulatus, a large isopod with direct development distributed in South Africa and Namibia. Individuals (n = 214) were sampled from 9 locations encompassing the entire distribution range, and sequence data were generated for mtDNA cytochrome c oxidase subunit I (COI) and 16S. Results revealed high levels of population structuring between populations (Phi(ST) = 0.11-0.96, p < 0.05), 2 deeply divergent lineages of T. granulatus and a new phylogeographic break in southern Africa. Northern populations are genetically more diverse, suggesting more stable evolutionary history compared to those in the south. Importantly, the patterns of divergence suggest unique evolutionary signals over short spatial scales (< 80 km), with nearly all T. granulatus populations effectively isolated from each other. This, in combination with increasing anthropogenic disturbance throughout their range, leaves this species extremely vulnerable to local, and potentially regional, loss and extinction of genetic diversity. We suggest that T. granulatus serves as a valuable bioindicator, which, if recognised for protection, will broadly capture biological and evolutionary patterns of other sandy beach macrofauna in the region. Our work adds to a growing field of sandy beach science, and contributes towards a better understanding of the significance, vulnerability and complexity of sandy beach ecosystems for conservation and management aims.