A ligand DNA including a probe portion having a sequence that is complementary to a target DNA to be detected in a sample DNA, and a probe portion having a base sequence that is complementary to a base sequence of a marker DNA 2 in a conjugate DNA 10 is formed, and the sample DNA and the ligand DNA are combined to form a DNA complex, and further, the DNA complex is made to perform electrophoresis in the conjugate DNA. Therefore, it is possible to provide a DNA separation detection method which can appropriately separate the sample DNA and deal with various kinds of target sample DNAs in short time, without the necessity of searching for an optimum electrophoresis condition by complicatedly combining the amount of a bonding control agent to be contained in the conjugate DNA, the viscosity of linear polymer, the amount of the sample DNA, the amount of the conjugate DNA, and the like, for each DNA sequence as a detection target, when separating the sample DNA by electrophoresis.