Abstract: Mangrove mud clam (Polymesoda erosa) has been proved to be an indicator specie in monitoring marine pollution by many studies in recent years. After postexposure treatment to Hexabromocyclododecane (HBCD) at 1,3,11,15 and 22 days and three concentrations(0.086, 0.860 and 8.600 μg/dm³),several genes encoded by mitochondria were selected from the upregulated cDNA library of the species, including cytochrome c oxidase subunit I,III (COX I、COX III),NADH dehydrogenase subunit I,III (ND I、ND III),cytochrome b(Cyt b) and inorganic pyrophosphatase (PPase). Realtime fluorescent quantitative PCR(qRT-PCR) is often used to study the tissue distribution and expression level of mRNA in such studies, however the technique is subject to considerable experimental error and variation. A stably expressed housekeeping gene (β-actin in this study) is needed as a reference gene to normalize the variation of target genes before performing qPCR analysis and comparison with control group.The result showed that expression of 6 genes could be detected and transcribed differently in all tissues after hexabromocyclododecane exposure.After statistic analysis, we found that compared with the control the expression of 6 genes in gill and hepatopancreas changed significantly,increased on the whole with the increase of exposure time and concentrations, but decreased when the exposure concentration was too high for the reason of limited stress ability of mitochondrion probably.Finally from the function of multienzyme complex in respiratory chain,reactive oxygen generation,ATP synthesis, and etc. we analyzed the reason for mitochondrial gene expression changes caused by HBCD exposure in order to lay a foundation for further study of molecular toxicology and development of molecular biomarkers in monitoring marine pollution in the near future.