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Cogon grass (Imperata cylindrica (L.) Beauv. var. major (Nees) Hubb.) is one of the top-ten weeds worldwide. It is also a C4 medicinal plant. In particular, an ecotype from Chuwei (CW) mangrove forest was found to be salt tolerant. Comparative proteomic analysis using two-dimensional (2D)-difference in gel electrophoresis coupled with liquid chromatography-mass spectrometry (LC-MS) was carried out to identify responsive leaf proteins in the CW ecotype and salt-intolerant Sarlun (SL) population following three days of 150 mM sodium chloride salt stress treatment. We identified five photosynthesis proteins including Rubisco small subunit, uncharacterized protein LOC100194054, Cyt b6-f, oxygen-evolving enhancer 2, and photosystem I reaction center subunit IV which were significantly up- or down-regulated by salt stress in CW ecotype but not SL population. Gene ontology enrichment analysis showed that photosynthesis was over-represented. The mass spectrometry proteomics data were deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD008482. Taken together, our proteomic study identified differentially accumulated proteins which provide additional evidence of ecophysiological variation in two natural variants of I. cylindrica.