Abstract: Counting accuracy of colonies is improved. A colony counting device captures a test individual to generate an image of the test individual, registers the image of the test individual in an initial state as a reference image, identifies a residue included in the reference image and identifies a position of the residue in a test image corresponding to the residue included in the reference image based on a displacement of each of two or more common characteristic portions between the reference image and the test image that is an image of the test individual after culturing, and counts the number of colonies while excluding the residue from a count as a colony based on the position of the residue.