Provided is a fluorescence observation apparatus including a fluorescence-image generating portion that generates a plurality of fluorescence images by capturing fluorescence from an observation subject at a time interval; a position identifying portion that, in the individual fluorescence images generated by the fluorescence-image generating portion, identifies high-luminance positions having gradation values equal to or greater than a predetermined threshold; a storage portion that stores the high-luminance positions identified by the position identifying portion; a track-image generating portion that generates a track image that has gradation values at the plurality of high-luminance positions stored in the storage portion; and a display portion that displays the track image generated by the track-image generating portion.