Provided is a method of determining a DNA tag which is a base sequence to be introduced into a genomic DNA sequence of an organism and an introduction site of the DNA tag into the genomic DNA sequence. The method includes: a step (S1) of obtaining a protein coding sequence of the genomic DNA sequence; a step (S2) of determining a region to be treated in the protein coding sequence; a step (S3) of fragmenting the coding sequence in the region to be treated; a step (S4) of subjecting the fragmented coding sequences to a silent mutation; a step (S5) of determining sequences suitable as primers from polynucleotides including the fragmented coding sequences or complementary base sequences thereof; a step (S6) of performing a homology search for the coding sequences thus determined; and a step (S8) of determining the determined coding sequence corresponding to a minimum value of an NMS as the DNA tag, and determining the site of the fragmented coding sequence corresponding to the determined coding sequence in the protein coding sequence as the introduction site.