Provided is a method comprising (A) fragmenting genomic DNA in a state where the interaction of the genomic DNA and molecules interacting therewith is maintained, and (B) bringing genomic DNA into contact with an exogenous molecule capable of binding to a specific endogenous DNA sequence in the genomic DNA. According to the method, with the use of an endogenous DNA sequence present inside or in the vicinity of a target genomic region in cells to be analyzed, any genomic region can be specifically isolated in a state where the interaction of the genomic region and molecules interacting therewith is maintained, without the need of inserting a recognition sequence of an exogenous DNA-binding molecule into the vicinity of the target genomic region in the cells to be analyzed.