The effect of substituents on in vitro activity of 20 1,8-naphthyridin-4-ones, a novel class of photosystem II inhibitors, was studied. A four-parameter QSAR model based on the molecular connectivity indices was developed which accounts for about 87% of the variations in inhibitory potencies of these compounds. The model suggests that the position, size, and polarity of substituents are factors that predominantly control their activity. By using physicochemical constants, a quantitative model for both 1,8-naphthyridin-4-ones and structurally related 2-trifluoromethyl-4-hydroxyquinoline derivatives was proposed.