1. An evaluation apparatus of fluorescent object population, comprising: an input unit inputting a fluorescence observation image of a fluorescent object population and a transillumination observation image having a same field of view as the fluorescence observation image; a first detecting unit detecting, as a first area, an area in which an object image exists on the transillumination observation image being input; a setting unit setting, as a reference area, an area corresponding to the first area on the fluorescence observation image being input; and an obtaining unit obtaining fluorescence intensity data of a fluorescence image from the reference area in the fluorescence observation image.