The development of non-invasive molecular techniques is currently increasing, particularly in the fields of behavioural ecology and conservation genetics of mammals. Surprisingly, genetic studies of Arthropods and particularly the insects have not benefited yet from the contributions that non-invasive methods have made. Here, we outline a strategy for identifying phytophagous insect genetic entities based on direct-PCR of fecal DNA combined with double strand conformation polymorphism (DSCP) typing. This allows the differentiation of morphocryptic entities within the species Ceutorhynchus assimilis (Coleoptera: Curculionidae), a candidate biocontrol agent of a noxious weed. The results obtained clearly demonstrate the potential for this method to provide a valuable means for genetic and ecological studies of Arthropods.