Functional, physicochemical and nutritional properties of protein from whole Klunzinger's ponyfish (Equulites klunzingeri) extracted by pH shifting methods were evaluated. The alkaline protein isolate (AlPI) had higher protein content (88.69 %) than the acid protein isolate (AcPI, 86.13%). AlPI had generally higher content of essential amino acid than AcPI, except methionine. The ratio of total essential amino acid/total amino acid in AlPI and AcPI of Klunzinger's ponyfish was found to be 47.5 and 44.9%, respectively. According to differential scanning calorimetry analysis, the T-max values of raw Klunzinger's ponyfish (R), AlPI and AcPI were determined to be 40.4, 71.2 and 70.44C, respectively. The initial thiobarbituric acid reactive substance value was higher in AcPI (1.99) than that in AlPI (1.19). AlPI was also found to be lighter and whiter than AcPI (L-star: 66.56, whiteness: 59.50 and L-star: 60.76, whiteness: 56.41, respectively). The results of "emulsion capacity," "water-and oil-holding capacity" and "foam capacity and stability" of AlPI and AcPI indicated that satisfactory functional properties are needed in food processing.