The microstructures of two layered films consisting of 2% Mn doped (Ba,Sr)TiO 3 (Mn:BST) and 2% Mn doped Ba (Zr, Ti)O 3 (Mn:BZT) layers on a MgO (001) substrate deposited by pulsed laser deposition were studied using X-ray diffraction (XRD), atomic force microscopy (AFM), transmission electron microscopy (TEM), high-resolution TEM and nanoindentation. The films contained four alternating layers of Mn:BST and Mn:BZT either the former or the latter as the first layer. The film deposited with Mn:BST as the first layer has a rough surface, an epitaxial continuous layer structure for the first two layers next to the interface and columnar structures for the top two layers. The first layer has a single oriented crystal structure with an in-plane lattice mismatch of ∼−5.70% and an atomically sharp interface with respect to the substrate. The second layer exhibited twin-induced domain structures. The columnar structures in the top two layers have an average width of ∼70 nm and are tightly attached to their adjacent grains without leaving any gaps or pores. The film deposited with Mn:BZT as the first layer has a relatively smooth surface and discrete needle-like nanopillars through the four layers from the interface to the top surface of the film. The first Mn:BZT layer consists of an epitaxial structure and its associated twin-coupled domains by sharing their {111} and {110} planes. The epitaxial Mn:BZT has an in-plane lattice mismatch of −3.34% with respect to MgO. The second, third and fourth layers have textured structures with {111} twin domains. The film deposited with Mn:BST as the first layer exhibited a higher hardness and modulus than the film with Mn:BZT as the first layer. The effects of the deposition sequence on the microstructure and mechanical properties are discussed.