Abstract Decades of research in population genetics have revealed that genetic divergence between populations and species is not uniformly distributed throughout the genome, but rather exhibits a high degree of heterogeneity. This phenomenon has sparked debate regarding the evolutionary mechanisms responsible for this variability. This study delves into the patterns of genomic divergence in populations of three marine limpet species, Scurria scurra, Scurria araucana, and Scurria ceciliana, which inhabit both sides of two biogeographic breaks (30-34°S and 41-43°S). To investigate this, genomic divergence was analyzed using estimates of FST and DXY with a 20 kb sliding window approach across the entire genomes of 56 individuals. Highly divergent genomic regions ranging from 20 to 280 kilobases in size were identified, primarily associated with the allopatric divergence model in all three species, although significant signals of divergence with gene flow were observed in some regions. Sympatric populations of S. scurra and S. araucana, spanning the 30-34°S latitudinal range, exhibited heterogeneous divergence patterns. In S. ceciliana, the southernmost species with populations across the 41-43°S latitudinal range, the allopatric divergence and divergence with gene flow processes seem to have deeply affected the genomic architecture of divergence. This pattern was not expected for this species with an evolutionary history of populations being isolated in glacial refugia. Genetic divergence appears to be species-specific, with few shared regions, and genes relevant to lipid metabolism, response to oxidative stress, and mitochondrial functions were identified within regions of divergence. These findings highlight the complexity of genomic diversification in marine limpets.