In a previous research we have studied the effect of the stimulation of the retina, by pulsed LED’s light of different wavelength, on the spectral density of the alpha rhythms of the electroencephalogram [1] [2]. In conformity to our results and the recent discovery of a nonvisual pathway of light from the retina to the brain, we are induced to search for the effect of stimulation of the retina, with different wavelength, on the melatonin’s secretion. We have, therefore, stimulated the retina with blue LED’s light 470 nm and red LED’s light 650 nm, and measured the melatonin’s secretion in saliva by means of High Pressure Liquid Chromatography (HPLC). The results show that melatonin values are higher with long wavelength stimulation (red, 650 nm) to be confronted with short wavelength stimulation where the values are lower (blue, 470 nm), the difference being significant (***). Action spectrum of short wavelength, producing melatonin suppression, was already evidenced in vivo; it was also demonstrated that blue LED’s light differentially modulated cell’s survival and growth, inducing mitochondrial suppression in vitro. We speculate, therefore, that long wavelength light (red) produces photobiomodulation effect at the level of the retina and that this effect is the opposite of the effect produced by the short wavelength (blue). The molecular mechanism underlying both effects may be, we suppose, the activation (red) or depression (blue) of the mitochondrial cytochrome c oxidase activity at the level of the pool of the retina’s ganglion cells.