Abstract We analysed the genetic divergence and morphology of the aedeagus (i.e. phallobase and parameres) in Canthon cyanellus at different geographical levels. The results from both approaches were compared with the current taxonomic assignment of the C. cyanellus complex, which includes three subspecies. We found a high variation in all the morphological characters of the aedeagus in the populations analysed; the morphometric variation was not geographically structured, either by population or by region. The genealogical analysis indicates a significant genetic structure that does not match either the morphological variation in the male genitalia or the previous subspecific taxonomic classification. Our results suggest that the morphological variation of the aedeagus is seemingly not an isolating reproductive barrier and that the intra- and interpopulation morphological variability of the aedeagus in the C. cyanellus complex does not permit the division into several species. We suggest that other evolutionary forces, such as genetic drift and sexual selection, have influenced the evolution of the male genitalia and the incipient differentiation of this species complex.