Coherent anti-stokes Raman scattering microscopy (CARS) was applied to visualize carotenoids in microalgae and cyanobacteria. Nonlinear light–matter interaction utilized in CARS microscopy inevitably induces a number of competing nonlinear processes, such as multiphoton excitation fluorescence. Microalgae and cyanobacteria being an intrinsically well-fluorescent object generates a strong two-photon-excitation fluorescence (TPEF) signal which should be effectively suppressed during the CARS experiment. Using an energetically balanced duel-wavelength excitation scheme and spectral purification of detecting signal, the TPEF was completely blocked providing a possibility to probe microalgae and cyanobacteria in a fingerprint region of the CARS spectrum. Microspectroscopy experiments were carried out with three species - cyanobacteria Nostoc Commune, Nostoc sp. and Chlorella sp. Distinct bands obtained in CARS spectra of such species were assigned to carotenoids and were taken as spectral markers in the imaging experiment. CARS imaging known as a chemical selective and label-free technique allows non-invasion monitoring of accumulation and movement of chemical compound at the subcellular level. Obtained high-resolution images of carotenoid distribution in algae and cyanobacteria clearly demonstrate the potential of CARS microscopy for spatially resolved analysis of the natural products stored in the microalgae and cyanobacteria cell. Copyright © 2013 John Wiley & Sons, Ltd.