Genetic analyses are widely used for a variety of ecological research scenarios, especially to aid species’ conservation programs. Where genetic material is required from rare or endangered spp. it is essential that the samples be collected non-destructively, the ultimate goal should be to develop reliable DNA extraction protocols that may be used with non-invasively collected samples. In this paper 3 methods of DNA extraction (DNeasy tissue kit, proteinase-K/TNES and Chelex-100) that use odonate (Coenagrion mercuriale) exuviae as a non-invasive source of genetic material are described and compared. DNA extracted from exuviae produced consistent genotypes at 5 polymorphic microsatellite loci for all of the samples processed using the DNeasy tissue kit and proteinase-K/TNES methods and 4 out of the 6 exuviae treated with Chelex-100. Exuviae offer an effective source of genetic material from endangered odonates and also highly mobile spp. that are too difficult to catch in significant numbers. As such, it is expected DNA extracted from exuviae to be widely applied to odonatological genetic research.