<p>Phylogenetic relations within <em>Aconitum </em>subgen. <em>Aconitum </em>(Ranunculaceae) in Europe are still unclear. To infer the phylogeny of the nuclear (ITS) region and chloroplast intergenic spacer <em>trn</em>L^(UAG)-<em>ndh</em>F of the chloroplast DNA (cpDNA), we analyzed 64 accessions within this taxon, 58 from Europe and six from the Caucasus Mts. Nuclear ITS sequences were identical in 51 European and two Caucasian accessions, whereas the remaining sequences were unique. cpDNA sequences could be categorized into five haplotypes, i.e., <em>A–E</em>, including a European-Caucasian <em>Aconitum </em>haplotype <em>B</em>. Ten cpDNA sequences were unique. A 5-bp indel distinguished the diploids from the tetraploids. None of the extant European diploids were basal to the tetraploid local group. A phylogenetic tree based on combined ITS and cpDNA sequences (bayesian inference, maximum likelihood, minimal parsimony) placed <em>Aconitum</em><em> </em><em>burnatii </em>(Maritime Alps, Massif Central) and <em>A. nevadense </em>(Sierra Nevada, Pyrenees) in a sister group to all other European species. A Bayesian relaxed clock model estimated the earliest split of the Caucasian species during the Late Miocene [ca. 7 million years ago (Mya)], and the divergence of <em>A. burnatii </em>and <em>A. nevadense </em>from the European genetic stock during the Miocene/Pliocene (ca. 4.4 Mya). Diploids in Europe are likely to be descendants of the Miocene European-Caucasian flora linked with the ancient Asian (arctiotertiary) genetic stock. The origins of the tetraploids remain unclear, and it is possible that some tetraploids originated from local, now extinct diploids. Both the diploids and tetraploids underwent rapid differentiation in the Late Pliocene – Quaternary period.</p>