A method of labeling an object is effective in attaching many species of labels according to the necessity to a minute object such as a fine particulate substrate that is used for fixing a probe molecule to be used in a bioassay. For a minute object, a labeling material prepared in accordance with a composition condition of contained atoms corresponding to at least binary n-digit of numerical information using a species number (n) of plural species of atoms selected in advance is used as a part of materials constituting the object and the presence or absence of the individual selected atoms or two or more content levels thereof is detected.