An exposure apparatus includes an atmosphere maintaining unit which maintains an exposure chamber in an air atmosphere, a gas supply unit which supplies air or a mixed gas containing air and an inert gas to a local space, between a final surface of a projection optical system and a substrate, a detector which detects an alignment mark and a reference mark formed on the substrate stage, and a controller. The controller controls the gas supply unit not to supply the mixed gas to the local space when the detector detects the reference mark, and controls the gas supply unit to supply the mixed gas to the local space when an instruction to detect the alignment mark upon setting the local space in a mixed gas atmosphere, and expose the substrate based on the detection results of the reference mark and the alignment mark is issued from the recipe.