Although several studies have evaluated the genetic structure and phylogeographic patterns in many species of marine invertebrates, a general model that applies to all of them remains elusive. For example, some species present an admixture of populations with high gene flow, whereas others exhibit more complex patterns characterized by small-scale unstructured genetic heterogeneity, even at a local scale. These differences are thought to be due to clear biological aspects such as direct versus indirect development, or the presence of lecithotrophic versus planktotrophic larvae, but few studies compare animals with similar distributions and life modes. Here, we explore the phylogeographic and genetic structure patterns in two chiton (Chiton olivaceus and Lepidopleurus cajetanus) and one abalone (Haliotis tuberculata) species co-occurring in the same habitat. Samples were obtained from shallow rocky bottoms along the Iberian Peninsula (Atlantic and Mediterranean coasts), Italy, Croatia and Greece, and the mitochondrial markers COI and 16S rRNA gene were sequenced. Our data show evidence of admixture and population expansion in C. olivaceus and H. tuberculata, whereas L. cajetanus exhibited a ‘chaotic patchiness’ pattern defined by a high genetic variability with locality-exclusive haplotypes, high genetic divergence, and a lack of geographic structure. Shared haplotypes were sampled in both coasts of Iberia (for H. tuberculata) and in the Western and Eastern Mediterranean (for C. olivaceus), potentially indicating high dispersal ability and a recent expansion. The processes underlying the fine-scale structuring in L. cajetanus remain a mystery. These results are especially interesting because the reproductive mode of the two chitons is similar but differs from that of the abalone, with a veliger larva, while instead the genetic structure of C. olivaceus and H. tuberculata are similar, thus contrasting with predictions based on the life history of the three molluscs and showing that the genetic patterns of marine species may be shaped by many factors, including historical ones.