PURPOSE: To markedly fast and sharply distinguish mutually complementary two polynucleotide sequences different in only one missed pair of sequences by subjecting plural polynucleotide chains containing two polynucleotide chains to their hybridization and then analyzing a change by reacting the hybridized polynucleotide chains with an exonuclease.

CONSTITUTION: A polynucleotide chain obtained by subjecting two or more kinds of polynucleotide chains containing at least two polynucleotide chains to their hybridization under proper conditions and a polynucleotide which is not subjected to hybridization are respectively allowed to react with an enzyme having exonuclease activity and the difference as the results of these reactions is analyzed to distinguish the mutually complementary two polynucleotide sequences different in one or more nucleotides. Furthermore, the enzyme having exonuclease activity is preferably an enzyme having 5'→3' exonuclease activity.