DNA was used as supramolecular scaffold to order chromophores and control their optical properties. Ethynylpyrene as energy donor was attached to 2′‐desoxy‐2‐aminoadenosine that binds selectively to thymidines (T) in the template. Ethynylperylene as acceptor was attached to 2′‐desoxyuridine that is complementary to 2′‐desoxyadenosine (A). This donor‐acceptor pair was assembled along single‐stranded DNA templates of different A−T sequences to investigate the sequence control of the energy transfer between the chromophores. The fluorescence intensities increase in the mixed assemblies along the DNA templates from A10T10 over (AATT)5 to (AT)10, although these templates provide equal numbers of potential binding sites for the two different nucleoside chromophore conjugates and exhibit similar absorbances. This shows that the sequence selective assembly of the two building blocks along DNA templates is programmable and alters the fluorescence readout. Such sequence‐controlled supramolecular chemistry represents the key element for future functional π‐systems in materials for light harvesting of solar energy.