Molecular evidence suggests that climatic fluctuations in the peninsulas of southern European during the Miocene and Pleistocene resulted in considerable genetic differentiation of organisms, probably following a ‘refugia within refugia’ model. We examined morphometric and meristic characters in museum specimens from the three Iberian clades of the smooth snake Coronella austriaca, previously described by molecular markers. We found sexual and interclade differences in scale counts and head shape. Sexes were dimorphic in the number of ventral and subcaudal scales, although sexual disparities in scale counts differed among clades. Moreover, discriminant and canonical analyses showed higher interclade differences in males than in females. The results obtained in the present study match those from molecular markers and confirm the population structure identified within Iberian C. austriaca. The observed sex discrepancy in this pattern suggests that males and females are subjected to different selective pressures along their Iberian distribution. In light of the above, C. austriaca may offer a useful model system in which to explore phylogeographical patterns in southern Europe, as well as the conflicts between processes driving morphological sexual divergence. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106, 210–223.