Our work is concerned with the occurrence and distribution of the sphalerite, wurtzite, and rocksalt phases, which can be present in the ZnMnSe system, and the analysis of structural defects. For this purpose, ZnMnSe layers with thicknesses between 700 and 1000 nm and Mn concentrations of 0%, 4%, 11%, 14%, 17%, 29%, 31%, 43%, 50%, 70%, 85%, and 100% were deposited by molecular-beam epitaxy on GaAs (001) substrates. The structure analyses were performed by transmission electron microscopy. A high density of stacking faults exceeding 10(9) cm(-2) is already present for a Mn concentration of 14% suggesting that lower Mn concentrations should be used for spin-aligning layers. A significant volume fraction of twinned regions is contained in the Zn0.69Mn0.31Se layer. ZnMnSe layers with Mn concentrations of 43%, 50%, and less than 30% consist exclusively of the sphalerite phase. The sphalerite and a small volume fraction of the wurtzite phase are contained in the sample with 31% of manganese. A mixture of the sphalerite, wurtzite, and rocksalt phases is observed for Mn concentrations of 70% and 85%. The presence of the wurtzite phase is correlated with regions, which contain particularly high densities of stacking faults. Only the rocksalt and the sphalerite phases remain for pure MnSe.