The microphase separated morphology of diblock copolymers can be used to generate well-ordered nanometer scale patterns over a large area. To achieve this goal, it is important to understand and control the behavior of diblock copolymer thin films on substrates, which can differ from the bulk behavior. We have investigated the morphologies and ordering in thin polystyrene-polybutadiene (PS-PB) diblock copolymer films on bare silicon and silicon nitride substrates, and also on polymethylmethacrylate (PMMA) coated substrates. The PS-PB copolymers are synthesized to form, in bulk, PB cylinders or spheres in a PS matrix. In thin films (10–60 nm thick), prepared by spin-coating, we observe that the morphology and ordering of the microdomains are affected by strong wetting constraints and a reduced chain mobility on the substrate. The thinnest self-assembled layer of the copolymer films shows no in-plane microphase separation on both types of substrates. The PS blocks wet the PMMA substrates whereas the PB blocks wet the bare substrates as well as the air interface. Hence, different film thicknesses are necessary on the two types of substrates to obtain a uniform film of the first self-assembled cylindrical or spherical microdomain layer. The first layer of the cylindrical copolymer can vary from cylindrical to spherical morphology with a few nanometer decrease in film thickness. In the case of spherical PS-PB diblock copolymer films, we observe that the ordering of the microdomains is improved in the films on the PMMA substrates, compared to those on the bare substrates. We also demonstrate a successful transfer of the microdomain patterns to silicon nitride substrates by a reactive ion etching technique.