Ductins represent membrane channel proteins which are supposed to form both proton channels in V-ATPases and connexon channels in gap junctions. In order to localize and characterize these proteins in different tissues of Drosophila, we applied indirect immunofluorescence microscopy and immunoblots, using antisera prepared against Drosophila ductin and against Nephrops ductin. Previously, these antisera have been shown to recognize, in ovarian follicles and young embryos of Drosophila, the ductin monomer of 16 kDa and a putative dimer of 29 kDa. Moreover, both anti-ductin sera label antigens in plasma membranes and in the cytoplasm and block, when microinjected, cell-cell communication via gap junctions. In the present study, comparing several embryonic, larval and adult tissues, the anti-ductin sera were found to recognize antigens with various locations in cells of the midgut, the salivary gland, the nervous system, the muscles and the epidermis. For example, in midgut cells, antigens were labeled mainly in apical plasma membranes and in the apical part of the cytoplasm, while in salivary-gland cells, labeling was found throughout the plasma membranes and the cytoplasm. We conclude that putative gap junctions were revealed in the salivary gland, the nervous system and the epidermis, while plasma membrane-associated putative V-ATPases were detected in the midgut, the salivary gland and the muscles. Moreover, V-ATPases associated with cytoplasmic vesicles were found in almost every tissue. On immunoblots of homogenates from various tissues, the anti-ductin sera specifically labeled bands of 16, 21 and 29 kDa. When comparing these bands using peptide mapping with V8 protease, we found that they represent closely related proteins. Therefore, either different ductins or modifications of a single ductin appear to be present in different cellular regions, cell types and developmental stages of Drosophila.