Genus Cheilosia (Diptera, Syrphidae) with more than 300 Palaearctic species is the most speciose group of hoverflies in Europe. One of the most widespread taxa with unclear taxonomic status is Cheilosia vernalis (Fallen, 1817). This species shows great morphological variation in external morphological characters. A subdivision of the taxon has been suggested, but the male terminalia of the different morphological forms appear identical. The aim of this study was to integrate the information from mitochondrial COI sequence data with re-evaluated morphological characters for exploring species boundaries and for revealing phylogenetic relationships of C. vernalis and closely related species. We sequenced a 698 bp fragment of the 3′-end of the mitochondrial gene cytochrome oxidase subunit I of 43 specimens agreeing with traditional morphological interpretation of C. vernalis (Diptera, Syrphidae), sampled from a broad geographic range in Europe and single representatives of 10 species of the vernalis—melanura complex. Parsimony analysis of the molecular data showed C. vernalis specimens grouped in three different lineages. The C. vernalis lineage presents 8 different mitochondrial haplotypes. We found no congruence between these haplotypes and diagnosable morphological characteristics of the adult fly specimens supporting species subdivision. Based on re-examination of type material two new synonyms are proposed: C. rotundiventris Becker, 1894 and C. ruficollis Becker, 1894 are junior synonyms of C. vernalis (Fallen, 1817). New diagnostic morphological character for C. reniformis Hellen, 1930 is added and first distribution data of this species in Europe are given. Taxonomic status of C. longifila Becker, 1894 remains unresolved.