This paper deals with the study of scytonemin in cyanobacteria applying coherent anti‐Stokes Raman scattering (CARS) microscopy. The chemically specific CARS response from particular chemical compounds in the algae cell is usually weak because of their low concentration and is often overwhelmed by optical emissions from other cellular constituents. This report demonstrates that for scytonemin localized in cyanobacteria Nostoc commune, the vibrational response is sufficient for its reliable identification. Scytonemin is known as a sunscreen sheath enclosing the cells of microalgae against ultraviolet radiation. The effectiveness of CARS microscopy as a mapping technique with the aim to visualize the scytonemin sheath in a live culture such as cyanobacteria N. commune has been revealed.