Euglena gracilis is an edible photosynthetic single-cell alga that can synthesize carotenoids. It is highly demanded to establish the technology to select and grow individual cells capable of synthesizing more carotenoids because it contributes to safe and inexpensive production of carotenoids. In the cells of E. gracilis, carotenoids are mainly contained in chloroplasts and eyespots, and typical carotenoids have a characteristic absorption maximum in common. E. gracilis also has an organelle resembling hematochrome, which has an appearance similar to the eyespot and the absorption band spectrally overlapping that of the carotenoid although reportedly it does not contain carotenoids. To discriminate the eyespot and hematochrome-like granules and to investigate the intracellular distribution of carotenoids, scan-free, non-invasive, absorbance spectral imaging A(x, y, λ) microscopy of single live cells was applied. It was demonstrated that this technique is a powerful tool not only for basic research on intracellular structural analysis but also for identifying difference in carotenoid content in individual cells applicable to screening of carotenoid-rich cells. By this technique, it was confirmed that carotenoids exist in chloroplasts and eyespots, and a number of characteristic absorption spectra of pigments observed specific to the eyespot or hematochrome-like granules were identified. In addition, it was found that hematochrome-like granules have a characteristic absorption peak at 620 nm as well as at 676 nm, suggesting that its origin is a component of chloroplast including Chlorophyll a.