In this study, magnesium (II) phthalocyanines (2a, 3a) and their water‐soluble derivatives (2b, 3b) were synthesized via multistep reactions. The structures of these phthalocyanines were identified by FT‐IR, NMR, MALDI‐TOF, and UV–Vis spectroscopy. The ct‐DNA binding (UV–Vis absorption, competitive EB binding, and agarose electrophoresis studies) and supercoiled plasmid DNA nuclease properties (hydrolytic, photonuclease, oxidative nuclease, and photooxidative nuclease) of the water‐soluble compounds were investigated using different methods. The DNA binding constant (Kb) values of 2b and 3b were calculated as 8.45 ± (0.25) × 104 and 7.71 ± (0.13) × 104 M−1 at 25°C, respectively. The results showed that 2b had a stronger ct‐DNA binding effect than 3b according to Kb and r values. The DNA nuclease studies claimed that both compounds indicated photonuclease activity on plasmid DNA depending on the light dose. Additionally, 2b had a higher photonuclease capacity than 3b. All of these results showed that 2b had promising potential as a photosensitizer agent for photodynamic therapy.