In insects, morphological species identification is often challenging. The discrimination of closely related species may be hampered when only subtle differences in phenotypic characters or a continuum in their variability are present. This is exemplified in the Cryptocephalus flavipes species complex (Coleoptera; Chrysomelidae) where, until now, the species have been discriminated only by the yellow pattern on frons, pronotum, and epipleurae. In the present study, the phylogeny of the C. flavipes species complex was resolved through a multi-locus sequence approach, and the inclusion in the group of the phenotypically similar Cryptocephalus quadripustulatus Gyllenhal, 1813 was evaluated. Subsequently, the C. flavipes species complex was used to test the usefulness of DNA-based approaches for species recognition and identification. All previously described morphospecies were recovered by means of species delimitation approaches. In addition, lineages of Cryptocephalus flavipes Fabricius, 1781 and Cryptocephalus bameuli Duhaldeborde, 1999, which have not evolved clear morphological differences, were found to form genetically well-isolated groups. A new taxon from Turkey was recognized as a separate lineage by DNA-based methods, and morphological diagnostic characters are reported. Through this study, new morphological diagnostic characters were discovered and the suitability of the meta-episternal shape in species discrimination was tested by a geometric morphometric approach.