Shifts in the magnesium to calcium ratio of seawater in the geological history are thought to have profoundly affected biomineralization of marine invertebrates, including some echinoderms, which changed their skeletal mineralogy from high-magnesium to low-magnesium calcite and vice versa. Here we report on experiments that aimed to investigate the effect of ambient seawater magnesium to calcium ratio on magnesium to calcium ratio and nanomechanical properties in the spines of two echinoid species (Arbacia lixula and Paracentrotus lividus). We found that echinoids cultured in seawater with a low magnesium to calcium ratio produced a skeleton with lower both magnesium content and nanohardness than those of the control specimens incubated under normal (high) magnesium to calcium ratio conditions. These results may suggest that at certain times in the geological past (during the so-called calcite seas) sea urchins with decreased skeletal magnesium contents were more susceptible to damage due to physical disturbances, predation and post-mortem taphonomic processes. Increased skeletal hardness of echinoids from the so-called aragonite seas is expected to enhance their taphonomic potential, thus, to some extent, mitigates the preservation bias related to increased solubility of high-magnesium calcite.