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The inner opercular membranes of the brackish medaka, Oryzias dancena, have numerous ionocytes, similar to the gill epithelia. By histological observation, this study demonstrated that it is possible to investigate the cellular morphology and function of ionocytes in the opercular membrane. The mitochondria-rich ionocytes in the opercular membranes were traced using rhodamine 123 and a cytochrome c oxidase IV antibody in vital and fixed situations, respectively. To validate different morphologies of seawater (SW)-type and freshwater (FW)-type ionocytes of the opercular membrane of euryhaline brackish medaka, a method of dual observation including immunofluorescence staining and subsequent scanning electron microscopy was used. The apical morphologies of SW- and FW-type ionocytes were hole and flat opening, respectively. In addition, the microvilli were found on the apical surface of the FW-type ionocytes. The SW-type ionocytes exhibited basolateral Na(+), K(+), 2Cl(-) cotransporter and the apical cystic fibrosis transmembrane conductance regulator. In contrast, in the apical region of FW-type ionocytes, Na(+), Cl(-) cotransporter and villin 1-like protein were expressed. In addition, histochemical staining of AgCl precipitation counterstained with a Na(+), K(+)-ATPase α-subunit antibody on the opercular membrane illustrated the role of Cl(-) secretion in the SW-type ionocytes of the brackish medaka. A combination of different observations in this study indicated that the opercular membrane could be a useful surrogate model for histological and functional studies on the epithelial ionocytes of fish gills.