A study of the Merodon taxa on the Balkan Peninsula, a region with a number of Pleistocene refugia, provides a useful framework for examining evolutionary processes and detecting hidden biodiversity. The phenotypic diversity of 22 samples of the Merodon ruficornis group on the Balkan Peninsula was examined using landmark-based geometric morphometrics. The boundaries of the species M. ruficornis, M. trebevicensis, M. auripes, M. armipes, and M. loewi were well defined based on wing shape and size. Canonical variate analysis showed that wing shape possessed sufficient differences to discriminate the species with a successful classification rate of 75–92% for males and 82–100% for females. The observed interspecific differentiation is generally in agreement with a previous study of the M. ruficornis group using a traditional morphological approach and molecular markers (allozyme loci, COI mtDNA). The spatial variability between conspecific populations and interpopulation variation were assessed based on both wing shape and size for male specimens. Phenotypically divergent units were delineated within previously defined species of the M. ruficornis group, indicating the possible presence of evolutionary independent units within the taxa analysed.