Calopteryx splendens is a widely distributed palaearctic damselfly with a remarkably uniform morphology. Variation in the size and shape of the pigmented spot on the wing is the main diagnostic character used to discriminate subspecies across its huge geographic range. Here, AFLP analysis was used to assess the genetic structure and diversity of nine populations representing 3 putative subspecies and evaluate the pigment spot as a taxonomic marker. Genetic diversity was high, with the number of polymorphic loci per population ranging from 141 to 280 out of a total of 333 variable sites (42.3-84.1%) and Nei's gene diversity from 0.160 to 0.283 (overall 0.299). Overall population genetic differentiation (FST = 0.2766) suggests limited gene flow and adaptation to local environments. Restricted gene flow and genetic differentiation among populations are supported by significant FST estimates. High levels of gene flow (Nm >1) were only recorded among three Asian populations (Russia - Kazakhstan - Turkey). The patterns of genotypic diversity suggest that a given wing spot size and shape may arise from the hybridization of a limited number, possibly not more than four, ancestral gene pools in different ways and at different times. Clearly, the sample analyzed was not sufficient to capture all of the complex history of C. splendens, but sufficient to indicate the taxa ancilla, waterstoni, and orientalis possibly represent three of the four ancestral gene pools, and originated in western Asia. The origin of the fourth, xanthostoma, is the western Mediterranean.