Over the last decade fluorescent reporter technologies (both fluorescent probes and proteins) have become a very powerful imaging tool in everyday biomedical research. Multispectral optoacoustic tomography (MSOT) is an emerging imaging technology that can resolve fluorophore concentration in small animals situated in deep tissue by multispectral acquisition and processing of optoacoustic signals. In this work, we study the optimum operating conditions of MSOT in imaging fluorescence activity in small animals. The performance of various fluorochromes / fluorescent proteins is examined and it is shown that the new infrared fluorescent protein is an order of magnitude brighter than the red ones. Finally, wavelength reduction after principle component analysis shows, that accurate unmixing and 3D reconstruction of the distribution of fluorochromes is possible only with 2 or 3 wavelengths.