Heavy metals are common pollutants in the freshwater environment and have toxicological effect in habitat organisms. The heavy metals highly accumulated in sediment and organism, and observed various physiological responses. In this study, we investigated the molecular response to heavy metal toxicity (Al, Aluminum; Cr, Chromium; Cu, copper; Mn, Manganese; Zn, Zinc) through expression of heat shock protein 40, 70, 90 (HSP40, 70, 90), cytochrome 450 (CYP450), Glutathione S-transferase (GST) and Serine-type endopeptidase (SP). HSPs showed up-regulation in Cu and Zn exposures. Furthermore, HSPs expression in treated groups tended to be higher than the control group. The tendency of CYP450 and GST mRNA expression was higher for Cr and Cu than for other exposure group. The expression of SP gene was low at Al exposure and other group were measured to be similar to control. These results suggest that heavy metal toxicity in freshwater ecosystem may affect physiological and molecular process. Also, the comprehensive gene expression in the aquatic midge Chironomus riparius give useful information to potential molecular biomarkers for assessing heavy metal toxicity.