Shewanella decolorationis S12 is capable of carrying out anaerobic respiration using azo dyes and Fe (III) citrate as electron acceptors. In the present study, proteomic techniques including two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry were used to analyze the similarity and the dissimilarity of the membrane proteins isolated from strain S12 cells grown in amaranth or Fe (III) citrate with defined inorganic salt medium. The cells of strain S12 grown under a saturated dissolved oxygen condition served as controls. This is the first work that made the comparative analysis of cell membranous proteomics of strain S12 grown with azo compound or Fe (III) citrate as a sole terminal electron acceptor. The results showed that most of the membrane proteins of strain S12 under azo respiration are similar to those under Fe (III) respiration, but dissimilar from those of oxygen-grown cells. FdnH and FrdB were expressed specifically in azo respiration. NqrA-2, DctP, and hypothetical protein SO_4719 showed relative overexpression in azo respiration compared with Fe (III) respiration. OmpA family protein SO_3545 was detected to be specific to Fe (III) respiration. Furthermore, ArgF, SdhA, and HoxK were expressed markedly in both amaranth- and Fe (III) citrate-grown cultures compared with oxygen-grown cultures.