Abstract‐The red pigment granule of Belpharisma japonicum is believed to be a photoreceptor organelle mediating photodispersal. Freeze‐fracture and thin section electron microscopy revealed that the pigment granules contained a honeycomb‐like structure constructed of folded membranes. In the fracture face of the honeycomb‐like structure, small membrane particles were observed, which might correspond to pigment—protein complexes. The pigment granules were isolated and detergent‐solubilized. Sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) showed that the pigment granules mainly contained a 200 kDa membrane protein. The complex of red pigment and 200 kDa protein was isolated by gel‐filtration chromatography of the detergent‐solubilized components, and the protein was subjected to SDS‐PAGE and amino acid analysis. The 200 kDa protein could not be dissociated into subunits by 2‐mercaptoethanol, indicating that the protein is composed of a single polypeptide chain. Hydrophobic amino acids contained in the 200 kDa protein were not dominant, suggesting that only partial domains may extend across the membrane of the honeycomb‐like structure.