A fluorescent signal analyzing apparatus includes an image input unit, a storage unit, an extracting unit, and an analyzing unit. At least one fluorescent image of a sample is input to the input unit. The storage unit stores data on the at least one fluorescent image input to the image input unit. The extracting unit extracts, for each of the fluorescent images, data on a fluorescence intensity in a desired region on the at least one fluorescent image from the data on the at least one fluorescent image stored in the storage unit. The analyzing unit calculates at least one of a correlation and a photon counting histogram for the desired region by use of the data on the fluorescence intensity.