Variation of 15 nuclear allozyme genes and a 708 bp fragment of DNA sequence of the mitochondrial cytochrome c oxidase subunit I (COI) gene were surveyed in a population of a hoverfly species, Merodon desuturinus Vujić, Šimić & Radenković, 1995 (Diptera, Syrphidae), endemic to the Balkan Peninsula. Based on phylogeography and taxonomy, Merodon desuturinus is of special interest from a biogeographical and conservation perspective. Characterization and determination of genetic relationships between M. desuturinus and taxa of the M. aureus, M. avidus, and M. ruficornis groups on the Balkan Peninsula were estimated based on molecular markers (allozymes and COI sequences). We observed that the mean number of alleles per allozyme locus was 1.1, frequency of polymorphic loci 0.067, and heterozygotes were absent. Our results showed an extremely low genetic variability in the M. desuturinus population sampled. We suggest that this taxon calls for a conservation management plan, as it is likely a vulnerable and threatened taxon, an endemic, spatially divided species and represents a unique genetic unit on the Balkan Peninsula.