Volcanic oceanic islands are some of the Earth’s most geologically and ecologically dynamic habitats, where continuous volcanic activity and erosion lead to the formation of habitats that drastically change throughout their ontogeny. Shallow-water sandy habitats, specifically, repetitively disappeared and regenerated due to seasonal oceanographic and climatic eustatic sea-level variations. For its inhabitants, these events translate into populations being cyclically removed or passing by drastic reductions in population size, where the outcome often depends on the specific life-history modes of the species, determining their dispersal, colonization potential and, ultimately, their survival ability. Therefore, population genetic patterns of marine shallow-water infaunal species can provide powerful clues of such outcomes, as well as how specific geological and ecological settings determine the genetic structure of the species. We herewith test the population structure of the marine infaunal bivalve Ervilia castanea (Montagu, 1803) in the sandy habitats of the Azores and Madeira Archipelagos (Northeast and Central Atlantic Ocean), by comparing insular populations with conspecifics from the nearest continental shores in mainland Europe. Little to no genetic structure was observed between insular populations with both nuclear microsatellites and the mitochondrial cytochrome c oxidase subunit I. Moreover, deviations in the Hardy-Weinberg Equilibrium of insular populations suggests the exitance of archipelago specific processes. The high dispersal ability of E. castanea combined with the ephemeral nature of oceanic shallow-water sandy habitats likely made each population to be composed of individuals from multiple sources. High prevalence of null alleles, gene duplication hint at the potential occurrence of recent polyploidization events that require further investigation. Moreover, we found evidence of hyperdiversity among the markers used which may constrain the detection of more detailed patterns. We herewith demonstrate the uniqueness of insular environmental settings and inquire further into the evolutionary and biogeographic patterns of marine shallow-water infaunal species from volcanic oceanic islands.