Heat shock proteins (HSPs) play an important role in adaption of environmental stress by protein folding, membrane translocation, degradation of misfolded proteins and other regulatory processes. Our previous study showed oxidative stress generated from polybrominated diphenyl ether-47 (PBDE-47) could cause an acute toxicity on freshwater bivalve Anodonta Woodiana, but the effect of chronic toxicity need to be elucidated. In order to further investigate the chronic effect of PBDE-47, clams A. Woodiana were randomly divided into the PBDE-47 treated group administrated with PBDE-47 at a concentration 3.36 μg/L and control group treated with a similar volume dimethyl sulfoxide. Two complete HSP sequences were isolated from A. Woodianaa and respectively named AwHSP60 and AwHSP70. They were widely distributed in foot, gill, hepatopancreas, adductor muscle, heart, hemocytes and mantle. Administration of PBDE-47 could result in a significant up-regulation of AwHSP60 and AwHSP70 expressions in the hepatopancreas, gill and hemocytes. In the hepatopancreas, compared with that of control group, mRNA level of AwHSP60 increased more than 89.9% (P < 0.05) from day 1–15, AwHSP70 increased more 2.79 times (P < 0.01). In the gill, during experiment observed, expression of AwHSP60 increased more 2.09 times (P < 0.01) in contrasted with that of control group. Significant up-regulation of AwHSP70 expression showed a reversed U shape. In the hemocytes, AwHSP60 and AwHSP70 expressions of PBDE-47 treated group respectively increased more 2.09 times (P < 0.05) and 1.81 times (P < 0.05) compared with that of control group. These results indicated that up-regulations of AwHSP60 and AwHSP70 expression are contribute to enhancing adaption of bivalve A. Woodiana exposed to PBDE-47 treatment.