Synthesis of heat shock proteins (Hsps) in response to elevated temperatures and other denaturing agents (including UV, heavy metals, and energy depletion) is a common productive response of prokaryotic and eukaryotic cells. Therefore, increasing in production of heat shock protein has been considered a sign of cells under stress. The phylum Sipuncula comprises of about 300 species worldwide; they are bilaterally symmetrical, unsegmented, and deposit feeding marine worms common in the substrate of wetland. In this research, I studied the dominant species Sipunculus nudus and analyzed it proteomics to reveal how it responses to persistent organic pollution. In order to compare the difference between HSP70 and HSP90, Sipunculans were sampling from two wetland (Xiangshan and Wanggong) in Hsinchu and Changhua,, respectively. The results showed that the concentrations of PAHs and OCPs both in substrate and S. nudus tissues from Xiangshan were higher than Wanggong. The concentrations of PAHs and OCPs in both areas showed that the environmental- sediment levels were higher than the sediment inside the gut or the body tissues. Principal component analysis showed that the compositions in S. nudus from both area were similar; however PAHs compositions from the environmental sediment or the sediment of the gut were similar. When the concentrations of HSP70 and HSP90 between both areas were compared, HSP70 expressions did not significant differed in both areas, while HSP90 express was higher in the S. nudus from Xiangshan than Wanggong. For S. nudus Hsp90 was upregulated in highly polluted area (i.e. Xiangshan). I propose that tissue expression of HSP90 plays an important role in the survival of S. nudus, and detection of HSP90 may provide pollution information of the surrounding environment.