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There are two different color strains in the budding ascidian, Polyandrocarpa misakiensis. One is spotless strain and the other is white-spot strain. A zooid of spotless strain has a white-band between branchial and atrial siphons. However, a zooid of white-spot strain has a clear white-spot between branchial and atrial siphons. Ishii et al. (1993) revealed that the differences between the color patterns of the two strains were mainly based on the distribution of red pigments in the epidermal cells. The area that lacks red pigments forms a fine white-band in the spotless strain or a circular white spot in the white-spot strain on the dorsal side. In this area, white pigment cells, which are distributed in the mesenchymal space, can be seen through the epidermal layer. In this report, red-orange pigments and white blood cells were examined with TEM. Also, by solubility test, the natures of pigments were studied. By TEM observation, red or orange pigments were thought to be the granules in the epidermal cells and white blood cells were the nephrocytes (one of blood cells). Solubility test revealed that the red-orange pigments are carotenoids and pteridines.