Provided is a method for specifically isolating any genomic region while maintaining interaction of the genomic region with its interacting molecule(s). According to the method comprising the following steps 1 to 5:Step 1: preparing a cell in which a DNA fragment having a recognition sequence(s) for an exogenous DNA-binding molecule is inserted in genomic DNA of a genomic region to be isolated; Step 2: bringing genomic DNA of the cell into contact with an exogenous molecule at least having a DNA-binding domain of the exogenous DNA-binding molecule; Step 3: performing a treatment for maintaining interaction of the genomic DNA of the cell with a molecule(s) interacting with the genomic DNA; Step 4: performing a treatment for fragmenting the genomic DNA; and Step 5: allowing a complex to be formed by binding of a molecule capable of specifically binding to the exogenous molecule, and then collecting the complex, specific genomic regions can be specifically isolated while kept interacting with their interacting molecules.