Synaptotagmins are Ca2+-and phospholipid-binding proteins of synaptic vesicles that might function as Ca2+ receptors for neurotransmitter release via their first C2 (C2A) domain. Here we describe the effect of Mg2+ on phospholipid binding to the C2A domains of multiple synaptotagmins (II-VI), and demonstrate that only synaptotagmin III can bind negatively charged phospholipids [phosphatidylserine (PS) and phosphatidylinositol] in a Mg2+-dependent manner. The Mg2+-dependent interaction with PS was found to have an EC50 of approx. 30 μM Mg2+, which is comparable to that of Sr2+ and Ba2+ (EC50 values of approx. 10 μM). This binding property of the C2A domain is specific to synaptotagmin III, because none of the C2A domains of other proteins, such as rabphilin 3A, Doc2α, Doc2β or Gap1m, showed phospholipid binding activity in the presence of 1 mM Mg2+. Our results suggest that synaptotagmin III is involved in presynaptic functions different from those of synaptotagmins I and II.