Patterns of genetic and morphometric differentiation were surveyed in Melitaea (Mellicta) athalia populations of the Carpathian Basin. This species has a wide distribution and exists under a wide variety of ecological conditions. It has two ecotypes in Hungary: with either one or two broods per year. It is of particular interest to reveal the main factors driving differentiation patterns in this species. Samples in our study were obtained from five Hungarian and one Transylvanian (Romanian) regions. Enzyme polymorphism, wing characters and male external genitalia were analysed using traditional morphometric methods. Statistical methods were optimized to compare morphological and genetic data. The results of genetic surveys revealed a clear regional pattern of differentiation in M. athalia. Moreover, the results of principal component analysis, Bayesian clustering and the dendrogram all suggested that the regions can be classified into two groups corresponding to the East or West zones of the Carpathian Basin. In contrast, differentiation between the two ecotypes was less expressed in the genetic variation of M. athalia. Results of the analyses conducted on phenotypic variation also suggested a regional pattern for both sets of morphometric characters (wings and external genitalia). At the same time, neither East–West regional division nor ecotype differentiation was detected in the morphometric studies. In sum, our analyses confirmed that both genetic and phenotypic variations of M. athalia exhibit a regional pattern rather than the differentiation between the two ecotypes. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.