The present invention relates to a method for detecting single nucleotide polymorphism (SNP) using a feature that the 5'-flap endonuclease (FEN) activity of DNA polymerase is inhibited when a probe complementarily binds to the end of a polymerase chain reaction (PCR) product. More specifically, the present invention relates to a novel method wherein it was verified that, when a probe used for a real-time PCR complementarily binds to the end site of a PCR product, the 5'-FEN activity of thermostable DNA polymerase to the probe is inhibited, and thus when such a feature is used to make a design such that an SNP site to be detected is located at the 5'-end site of the probe, the 5'-flap formation is induced according to the allele, thereby allowing effective SNP detection.
