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Background and aims – Chaerophyllum hirsutum represents a complex of taxa with varying treatments and ranks across floras. Using both morphometric and molecular markers, we assessed the robustness of C. hirsutum, C. elegans, C. villarsii, and C. villarsii var. cicutariiforme. Material and methods – Ten morphometric variables and two ratios were calculated. Based on the sequencing of six plastomes, the rps16 intron was selected as the more variable region and sequenced on a broader sampling. Additionally, we also sequenced the nrDNA internal transcribed spacer 2 (ITS2) using Illumina technology to obtain intra-individual allelic diversity. Key results – Morphologically, the most easily differentiated taxon was C. elegans, especially using the number of subterminal umbels. The distinction between C. hirsutum and C. villarsii was rather clinal, but is mainly based on the degree of carpophore division. Finally, C. villarsii var. cicutariiforme was less easily distinguishable from the three others, but partly using the carpophore length and the total length of basal leaf blade. The cpDNA rps16 clearly distinguished C. elegans from the three other taxa of the complex, which rather showed a geographical pattern of cpDNA diversity. The nrDNA ITS2 partially distinguished C. villarsii from the other taxa, without distinction of C. elegans. Conclusions – The present study supports the species differentiation of C. elegans based on both morphology and chloroplast genome. Furthermore, C. villarsii var. villarsii and C. villarsii var. cicutariiforme could potentially be recognized as distinct varieties within C. hirsutum. This will need to be confirmed by future studies using a larger sampling size and more comprehensive markers, covering a broader portion of the nuclear genome.