Avicennia marina(Forsk.) Vierh. is a typical mangrove plant. Its epidermis contains salt glands, which can secrete excess salts onto the leaf surfaces, improving the salt tolerance of the plants. However, knowledge on the epidermis-specific transcriptional responses ofA. marinato salinity treatment is lacking. Thus, physiological and transcriptomic techniques were applied to unravel the salt tolerance mechanism ofA. marina. Our results showed that 400 mM NaCl significantly reduced the plant height, leaf area, leaf biomass and photosynthesis ofA. marina. In addition, 1565 differentially expressed genes were identified, of which 634 and 931 were up- and down-regulated. Based on Kyoto Encyclopedia of Genes and Genomes metabolic pathway enrichment analysis, we demonstrated that decreased gene expression, especially that ofOEE1,PQL2,FDX3,ATPC,GAPDH,PRK,FBPandRPE, could explain the inhibited photosynthesis caused by salt treatment. Furthermore, the ability ofA. marinato cope with 400 mM NaCl treatment was dependent on appropriate hormone signalling and potential sulfur-containing metabolites, such as hydrogen sulfide and cysteine biosynthesis. Overall, the present study provides a theoretical basis for the adaption ofA. marinato saline habitats and a reference for studying the salt tolerance mechanism of other mangrove plants.