© 2015 Wiley Periodicals, Inc.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 Tmax 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*: 66.56, whiteness: 59.50 and L*: 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. Practical Applications: Klunzinger's ponyfish is a discard fish that exists in large amount in Mediterranean Sea. Even if it has a potential as high quality protein source, it is not being used for human food products as functional ingredients. This study investigates the functional, physicochemical and nutritional properties of protein from whole Klunzinger's ponyfish extracted by pH shifting methods. According to the obtained data in this study, the nutritional, functional and physicochemical properties of protein isolates of Klunzinger's ponyfish were suitable for supplementing as an ingredient for human consumption. Protein as an ingredient developed from an inexpensive source is important to the industry.