To provide a method whereby a region containing a binding site of a DNA capable of binding to a DNA-binding protein in the DNA can simply and quickly be detected.

Provided is the method characterized by comprising: preparing a first liquid mixture containing a fluorescent labeled DNA-binding protein and a first DNA known as being bound by the above protein and a second liquid mixture containing a second DNA and a fluorescent labeled DNA-binding protein; determining the presence or absence of a difference in motion speed between the DNA-binding protein in the first liquid mixture and the DNA-binding protein in the second liquid mixture on the basis of the fluorescence intensities of the first and second liquid mixtures; and detecting the region containing the binding site of the DNA on the basis of the results.