An image acquiring apparatus is made up of a macro image acquiring unit 20 used to acquire a macro image of each of a plurality of samples S, and a control unit 60 including a macro image acquisition control unit used to control a macro image acquiring operation and an image pickup condition setting unit used to set an image pickup condition for a micro image of the sample S with reference to the macro image. The control unit 60 includes a session managing unit used to define a session in accordance with a sample group consisting of the samples S and to manage a data group including data of the macro image and the image pickup condition as session data associated with the sample group for each session. According to this structure, it is possible to realize an image acquiring apparatus, an image acquiring method, and an image acquiring program capable of suitably managing image acquisition processing performed to acquire an image of each of a plurality of samples.