Eucheuma cottonii is a red seaweed of the family Rhodophyceae, which is mainly harvested in South East Asia. E. cottonii has long been explored as a major source of kappa carrageenan, which is of great economic and industrial importance. The proteomics of marine macroalgae is always a tough task due to low protein concentration and a greater possibility for the co-extraction of contaminants such as anionic polysaccharides, polyphenols and salts, which may massively deteriorate the resolving power of SDS-PAGE and current proteomic tools. The main objective of this study is to compare three different phenol based protein extraction protocols: (i) Phenol/lysis buffer extraction, (ii) TRI reagent/ chloroform extraction, and (iii) Phenol/SDS buffer extraction in terms of total protein yields and resolving patterns of single dimension SDS-PAGE. Among the three phenol based extraction protocols, the phenol/lysis buffer produced slightly higher protein yields (0.027±0.000 mg/g), followed by the phenol/SDS buffer (0.024±0.002 mg/g) and the TRI reagent/chloroform (0.018±0.001 mg/g). In SDS-PAGE, all the three extraction protocols showed clear protein profiles, with several intense protein bands observed from 27 kDa to 158 kDa. The phenol/SDS buffer extraction protocol was recommended for proteome study of E. cottonii as it is the cheapest and relatively easy in preparation as compared to the other two protocols in this study. This study represents an initial attempt to study the proteome of E. cottonii. Further proteomic works, such as two-dimensional gel electrophoresis, mass spectrometry and protein crystallography, can be carried out in the near future. A successful establishment of E. cottonii proteome is important to facilitate the exploration of E. cottonii and other carrageenan rich seaweed species due to its agricultural significance.