In acquisition of a micro image of a sample S by a micro image acquiring unit, when a plurality of image acquiring ranges are set for the sample S as an object of image acquisition, a plurality of corresponding focus information are set, and furthermore, when a plurality of partial images acquired by scanning the sample S by the micro image acquiring unit include a partial image including mixing of a plurality of image acquiring ranges, the focus information is switched in the middle of scanning of the partial image. With such a structure, even when a plurality of objects are contained in the sample S, images of the respective objects can be preferably acquired. Thereby, an image acquiring apparatus, an image acquiring method, and an image acquiring program which are capable of preferably acquiring images of a plurality of objects are realized even when the plurality of objects are contained in a sample S.