Organisms in different environmental conditions express different genes, which result in different protein expressions. These changes result from the adaptation of the organism to environmental conditions such as the presence of toxic substances. This study aimed to investigate the changes in protein expression in Celeribacter persicus SBU1 isolated from Nayband Bay mangrove forests, cultured in the medium containing phenanthrene as the sole source of carbon and energy. For this purpose, C. persicus SBU1 was cultured on mineral salt medium containing phenanthrene and sodium acetate as treatment and control, respectively. After the extraction of total protein, changes in protein expression were evaluated by SDS-PAGE. Proteins were identified by MALDI-TOF-TOF MS. After evaluating changes in protein content, two bands which showed greater variation in comparison with the control treatment (increased protein expression) were detected. The identified proteins included one ligand-gated channel protein and one unknown protein. In general, the results of this study showed significant changes in the protein content of C. persicus SBU1 after using phenanthrene. The up-regulation of ligand-gated channel protein signified the role of this protein in phenanthrene molecules transport in and out of the cells.