For the health levels of the tidal flat and manila clam, (Ruditapes Philippinarum) in the west coast of Korea, the habitat characteristics of tidal flat and the biomarker genes of manila clams were investigated. Surface sediments and manila clams were collected from eight site of west coast of Korea, they were examined the geochemical characteristics and manila clams were analyzed the Poly Aromatic Hydrocarbons (PAHs) and heavy metals and the total RNA of these meat part with RT-qPCR method. Total RNA such as heat shock protein 70 (Hsp70), heat shock protein 90 (Hsp90), glutathione S-transferases (GST) and thioredoxin (TRX) was extracted from the meat part of the collected clams. Expression of the genes was analyzed by PCR method and the expression of biomarker genes were changed in the eight sites analysis areas. These results indicate that biomarker genes can be used to assess the condition of the environment. That is related to stress, immune and antioxidant related genes. Results showed that the expression of biomarker genes were changed in the eight sites and were relevant with the heavy metals and PAHs concentration of sediments, respectively. We suggested that biomarker genes were impressed an important role for the health level assessment of tidal flats.