Phthalocyanines are promising photosensitizers for use in various branches of science including nanotechnology. In the presence of visible light and diatomic oxygen, phthalocyanines can react to produce singlet oxygen (1O2*), which has known inhibitory effects on cellular growth and metabolic activity, although other mechanisms may be involved. The present work focuses on the properties of phthalocyanines (atom charge densities, singlet oxygen production, inhibition effects at various irradiances) contributing to toxicity against the cyanobacteria, Synechococcus nidulans. Our results indicate that positive charge densities at peripheral parts of substituents exhibit greater inhibitory effects against S. nidulans than the amount of singlet oxygen produced, potentially by binding to negatively charged membranes on the cell surface. The weak effect of 1O2* was further demonstrated by a 10% increase in phthalocyanine toxicity (the maximal inhibition detected) when the irradiance increased 3-fold from 1200 to 4000 lux.