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In the title complex, [Zn(C3H2O4)(C12H8N2)2]·5H2O, the ZnII cation displays a distorted octahedral geometry, being coordinated by four N atoms from two 1,10-phenanthroline ligands and two O atoms from different carboxylate groups of the chelating malonate dianion. In the crystal, the complexes are linked into a three-dimensional supramolecular network by both O—H...O hydrogen-bonding interactions between water molecules and the uncoordinated carboxylate O atoms of neighboring molecules, and aromatic π–π stacking interactions between neighboring phenanthroline rings with centroid–centroid distances of 3.4654 (17) and 3.697 (2) Å.