The phylogeographic pattern of the temperate shrub Lonicera nigra (Caprifoliaceae) in Europe was inferred from molecular and fossil data. Population samples and pollen data from most of the contemporary natural distribution were analysed. While chloroplast DNA sequences revealed no intraspecific variation, AFLP data show a non-random geographic pattern. Two genetically different groups, distinguished by Bayesian clustering, divided the distribution area of L. nigra into south-western and north-eastern regions with a contact zone situated approximately in the upper part of the Danube Valley. Iberian populations constitute an additional distinct genetic group. Pollen evidence supports the genetic data, indicating that L. nigra might have survived in glacial refugia located in Central Europe. Nevertheless, this evidence should be considered only as indicative and supplementary, as an unambiguous determination of the species is not possible based on the information on pollen in the literature.