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We report transmission electron microscopy studies of native extended defects in pseudomorphic ZnSe/GaAs (001) and lattice-matched ZnSe-In0.04Ga0.96As (001) heterostructures. The dominant defects present in the layers were identified as Shockley stacking fault pairs lying on (111) and fault planes and single Frank stacking faults lying on or fault planes by comparing experimental images with the predictions obtained with the g.b = 0 rule as well as with simulated images.