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Cetaceans are recognized as bioindicators of pollution in oceans. These marine mammals are final trophic chain consumers and easily accumulate pollutants. For example, metals are abundant in oceans and commonly found in the cetacean tissues. Metallothioneins (MTs) are small non-enzyme proteins involved in metal cell regulation and are essential in many cellular processes (cell proliferation, redox balance, etc.). Thus, the MT levels and the concentrations of metals in cetacean tissue are positively correlated. Four types of metallothioneins (MT1, 2, 3, and 4) are found in mammals, which may have a distinct expression in tissues. Surprisingly, only a few genes or mRNA-encoding metallothioneins are characterized in cetaceans; molecular studies are focused on MT quantification, using biochemical methods. Thus, we characterized, in transcriptomic and genomic data, more than 200 complete sequences of metallothioneins (mt1, 2, 3, and 4) in cetacean species to study their structural variability and to propose to the scientific research community Mt genes dataset to develop in future molecular approaches which will study the four types of metallothioneins in diversified organs (brain, gonad, intestine, kidney, stomach, etc.).