In order to assess the health level of tidal flat, we investigated heavy metals of surface sediments and the biomarker genes of Ruditapes philippinarum samples in the west coast of Korea. Manila clams were collected from 8 sites of western coast and analyzed the total RNA of these meat part with RT-qPCR method. We have examined the geochemical characteristics of surface sediments and the concentration of inorganic elements of manila clam with XRF. It is possible for the health level of inhabit organisms using analysis of expression of biomarker genes such as heat shock protein 70 (Hsp70), heat shock protein 90 (Hsp90), glutathione S-transferases (GST) and thioredoxin (TRX). That is related to stress, immune and antioxidant related genes. Results showed that the expression of biomarker genes were changed in the 8 sites and were relevant with the heavy metal concentration of sediments, respectively. We suggested that biomarker genes were played an important role for the health level assessment of tidal flats.