Current non-invasive imaging methods of fluorescent molecular probes in the visible and near-infrared suffer from low spatial resolution as a result of rapid light diffusion in biological tissues. We show that three-dimensional distribution of fluorochromes deep in small animals can be resolved with below 25 femtomole sensitivity and 150 microns spatial resolution by means of multi-spectral photo-acoustic molecular tomography. The low sensitivity limit of the method is enabled by using the highly resonant absorption spectrum of a commonly used near-infrared fluorescent molecular probe Alexa Fluor 750 in order to acquire differential images at multiple wavelengths with tomographic topology suitable for whole-body small animal imaging.