Organisms that live in marine, estuary and fresh ecosystems are often exposed to anthropogenic influence. Among the pollutants, metals are of major concern because they are not biodegradable. Bivalves are filter-feeding organisms and accumulate high levels of heavy metals. Therefore, they are widely used as bioindicators of metal contamination. Exposure to toxic metals is stressful because metals can bind to essential biomolecules. Therefore, bivalves develop detoxification mechanisms to remove metals from the vicinity of important molecules. This may be achieved by binding metals to metallothioneins (MT-s). MT-s are cytosolic low-molecular weight proteins which are responsible for maintaining homeostasis of essential (Zn, Cu) and detoxification of non-toxic metals (Cd, Hg, Ag). These metals are inducers of MT synthesis and bind on MT. Induction of MT is considered as biomarker of metal exposure. MT-s are used as biomarkers in biomonitoring because they are early-warning indicators of pollution and signal harmful effects of contaminants. The uptake of metals may take place via gills, digestive gland or via the surface of the mantle so level of MT is measured in them. However, many biotic and abiotic factors can influence higher synthesis of MT. Therefore, it is necessary to distinguish between the impact of environment factors and anthropogenic contaminants. Also, MT response to metals depends on the organism, the tissue examined and the MT isoform studied. Applying MT-s in bivalves as biomarkers of metal exposure is useful in many ecotoxicological studies and is of great importance to assess level of contamination in aquatic environment.