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We tested the usefulness of exuviae as an environmentally friendly method for exploring the variability of the trace element contents of protected insect populations without killing specimens. It is a notable characteristic of dragonflies that they are good ecological indicators for both aquatic and terrestrial habitat quality. Thus, we investigated the trace element accumulation in different stages of dragonflies: larva, exuvia, and adult. Using microwave plasma atomic emission spectrometry (MP-AES), we analysed the concentrations of Al, Ba, Cr, Cu, Fe, Mn, Pb, Sr and Zn. We found that the trace element contents of exuviae are a good proxy of the trace element contents of both the larvae and the adults. We conclude that exuvia is useful for assessing the environmental health of aquatic ecosystems. It is an environmentally friendly method and it can be used even in the case of protected dragonfly species.