Giant mudskipper(Periphthalmodon schlosseri, Pallas 1770)is one of important biological diversity that potential as bio-indicator in environment assessment which isheavy metal contamination. These fish are susceptible to ambient environment, that effect to their physiological mechanism including protein synthesis and expression. Thisresearch aims to identify protein profiles of giant mudskippermuscleand review its potential application as a biomarker for heavy metal contamination in Barito Estuaryof South Kalimantan. Total proteins were isolated from fish muscle using Tris EDTA buffer and then precipitated using Ammonium sulfate salt. The protein concentration was measured using Bradford assay and then separated based on molecular weight using the SDS-PAGE method. The result showed muscle proteins of giant mudskipper could be precipitated on optimum condition at Ammonium sulfate saturation 60-70% whichprotein concentration 5.106mg.mL-1. The protein separated into 20 bands for raw and precipitated proteins which molecular weight ranging from 33 into 184 kDa. Further study is neededfor protein identification based on amino acids sequence of protein bandsfor biomarker discovery and validation.