The type of a nucleotide located in a mutation site on a target nucleic acid can be identified by carrying out a fluorescence real-time PCR using a probe set comprising a detection probe and a counter probe, wherein the detection probe comprises an oligonucleotide which comprises a nucleotide sequence containing the mutation site on the target nucleic acid and also containing a nucleotide of interest in the mutation site or a nucleotide sequence complementary to the aforementioned nucleotide sequence, has a fluorescent substance added to the 5-terminal and a quenching substance added to the 3-terminal, and has, introduced therein, such a modification that the melting temperature of the probe becomes 3°C or more higher than that of the counter probe, and wherein the counter probe comprises an oligonucleotide which comprises a nucleotide sequence containing a mutation site and also containing a nucleotide that is different from the nucleotide of interest in the mutation site or a nucleotide sequence complementary to the aforementioned nucleotide sequence.
