The ability of the DNA duplex to behave as an efficient organized medium for trans–cis photoisomerization has been explored. The presence of DNA affected isomerization in a variety of ways depending on the aryl moiety properties of the ligand and its DNA-binding mode. Contrary to intercalating ligands, 9-[2-(N-methylpyridinium-4-yl)vinyl]phenanthrene (2) and 9-[2-(N-methylpyridinium-4-yl)vinyl]anthracene (3), which gave only cis and trans isomers, the additional products—cyclobutane photodimers—were detected for 2-[2-(N-methylpyridinium-4-yl)vinyl]naphthalene (1), which binds cooperatively to the minor groove of DNA. Photostationary states (pss) for all ligands were seriously affected by the presence of DNA. A trans isomer–rich pss and restriction of trans → cis process, observed for ligands 1 and 2, were explained in terms of a different binding affinity of DNA toward particular isomers. On the contrary, 9-anthryl derivative 3 isomerized against the isomer-binding preferences, showing cis isomer–rich pss and enhanced quantum yield of isomerization. The unique behavior of ligand 3–DNA complex was attributed to different isomerization mechanism that consists in quantum chain isomerization from an excited singlet state possessing a charge transfer character. This is the first example of ligand, which undergoes DNA-mediated cis–trans isomerization in the opposite direction than expected from DNA-binding preferences. The analysis of pss data based on two alternative pathways of photoisomerization showed that investigated ligands follow the model that allows isomerization of both free and DNA-bound ligands.