Insect genital characters are extensively used in species level taxonomy, and their value in species delimitation is great. Based on the lock-and-key hypothesis and that genital differences function as a mechanical isolation system between species, the value of genital characters has been thought to be superior to non-genital characters. Although geographical and other kind of intraspecific variation of genitalia is often assumed very moderate, its real extent is insufficiently investigated. We examined patterns of morphological variation in the male genitalia of the tortricid moth Pammene luedersiana, using geometric morphometric tools including thin-plate spline deformation grids, and found significant variation. This variation is continuous both within and between populations. No systematic shape variation was observed between populations, but genital size showed some geographic variability. The results suggest that genital morphology is not constant and should therefore be used with caution in lepidopteran taxonomy.