An alignment apparatus according to one embodiment, includes: a first and a second stage; a first and a second detector; a first and a second moving mechanism; and a controller. The first and second stages are configured to respectively hold a first and a second semiconductor substrate on which a first and a second alignment mark are respectively disposed. The first and second moving mechanisms are configured to respectively move the first and second stages relatively to each other. The controller is configured to perform the following (a), (b). (a) The controller control the detectors and the moving mechanisms to cause the first detector to detect the second alignment mark and to cause the second detector to detect the first alignment mark. (b) The controller calculate a position deviation between the substrates in accordance with results of the detections.