Transmission electron microscopy characterization of two major long-period stacking ordered (LPSO) phases in Mg–Zn–Y alloy, i.e., 18R- and 14H-LPSO are reported. The space group and atomic-scale microstructures of both compounds were determined using a combination of electron diffraction, convergent beam electron diffraction, high-resolution transmission electron microscopy, and Z-contrast scanning transmission electron microscopy. The 18R-LPSO phase is demonstrated to have a point group and space group 3m and R3m (or 3
m and R
m), with the lattice parameter a = 1.112 nm and c = 4.689 nm in a hexagonal coordinate system. The 14H-LPSO phase has a point group 6/mmm and a space group P63 /mmc, and the lattice parameter is a = 1.112 nm and c = 3.647 nm. In addition, insertion of extra thin Mg platelets of several atomic layers, results in stacking faults in the LPSO phase. These results may shed some new light on a better understanding of the microstructure and deformation mechanisms of LPSO phases in Mg alloys.