An electrophoretic separation data analyzing apparatus includes an analysis target peak identifying part configured to require a user to input analysis target peak information on analysis target peaks to be added to an analysis target in separation data obtained by electrophoretic separation, and to identify at least one of the analysis target peaks based on the analysis target peak information, a peak-of-interest identifying part configured to require the user to input peak-of-interest information on a peak of interest among the analysis target peaks, and identify the peak of interest based on the peak-of-interest information, and an abundance ratio calculating part configured to determine an abundance ratio of the peak of interest among all of the analysis target peaks based on a total value of peak areas of the analysis target peaks and a peak area value of the peak of interest.