Cidaroid sea urchins are the sister clade to all other extant echinoids and have numerous unique features, including unusual primary spines. These lack an epidermis when mature, exposing their high-magnesium calcite skeleton to seawater and allowing the settlement of numerous epibionts. Cidaroid spines are made of an inner core of classical monocrystalline skeleton and an outer layer of polycrystalline magnesium calcite. Interestingly, cidaroids survived the Permian-Triassic crisis, which was characterized by severe acidification of the ocean. Currently, numerous members of this group inhabit the deep ocean, below the saturation horizon for their magnesium calcite skeleton. This suggests that members of this taxon may have characteristics that may allow them to resist ongoing ocean acidification linked to global change. We compared the effect of acidified seawater (pH 7.2, 7.6, or 8.2) on mature spines with a fully developed cortex to that on young, growing spines, in which only the stereom core was developed. The cortex of mature spines was much more resistant to etching than the stereom of young spines. We then examined the properties of the cortex that might be responsible for its resistance compared to the underlying stereomic layers, namely morphology, intramineral organic material, magnesium concentration, intrinsic solubility of the mineral, and density. Our results indicate that the acidification resistance of the cortex is probably due to its lower magnesium concentration and higher density, the latter reducing the amount of surface area in contact with acidified seawater. The biofilm and epibionts covering the cortex of mature spines may also reduce its exposure to seawater.