Morphological and genetic data are increasingly used in combination to test taxonomic hypotheses of species status. We compared the morphological and genetic diversity of the spring-dwelling crane fly, Pedicia occulta (Diptera), a widely distributed western Palearctic species considered to be monotypic throughout its range. We studied 11 morphological characters from 360 male individuals from the entire recorded range of P. occulta, and analyzed a subset of 77 individuals from the southeastern Carpathians, Rila, Pirin, and Rhodope for genetic variation at the mitochondrial cytochrome c oxidase I subunit (COI) gene. In contrast to expectations, our data on morphology and genetic structure of populations showed a structured pattern in the Carpathian region. Two well-separated groups were identified with nonmetric multidimensional scaling based on morphology. COI data revealed 2 divergent lineages (13.4% sequence distance) that corresponded to the 2 morphological groups and to differences in phenology and behavior. Sequence data showed additional genetic subdivision within one of these morphological groups, perhaps indicating the existence of additional cryptic entities. Our results also point out the importance of the Carpathian spring and mountain aquatic ecosystems as Pleistocene refugia. Our study emphasizes the power of combining morphological, genetic, and behavioral approaches in taxonomic hypothesis testing.