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UV radiation, desiccation, and starvation induce some cyanobacteria to produce a UVA-absorbing pigment, scytonemin, at extracellular sheaths. Although the accumulation of scytonemin is recognizable as dark sheaths through optical microscopes, it has been nontrivial to identify its redox status and obtain its subcellular distribution in response to physiological conditions. Here, we show that a spontaneous Raman scattering spectral microscopy based on an excitation-laser-line-scanning method unveil 3D subcellular distributions of non-UV-induced scytonemins with distinct redox statuses in a filamentous cyanobacterium with a single nitrogen-fixing cell at the basal end. Cellular differentiations and scytonemin redox conditions were simultaneously visualized with an excitation wavelength at 1064 nm that is virtually free from the optical screening by the dark sheaths. The molecular imaging results give insights into not only secretion mechanisms of the sunscreen pigment but also interdependence between photosynthesis, nitrogen fixation, and redox homeostasis in one of the simplest forms of multicellular organisms.