Recent phylogenetic analyses of the Dipsacales strongly support a Caprifolieae clade within Caprifoliaceae including Leycesteria, Triosteum, Symphoricarpos, and Lonicera. Relationships within Caprifolieae, however, remain quite uncertain, and the monophyly of Lonicera, the most species-rich of the traditional genera, and its subdivisions, need to be evaluated. In this study we used sequences of the ITS region of nuclear ribosomal DNA and five chloroplast non-coding regions (rpoB–trnC spacer, atpB–rbcL spacer, trnS–trnG spacer, petN–psbM spacer, and psbM–trnD spacer) to address these problems. Our results indicate that Heptacodium is sister to Caprifolieae, Triosteum is sister to the remaining genera within the tribe, and Leycesteria and Symphoricarpos form a clade that is sister to a monophyletic Lonicera. Within Lonicera, the major split is between subgenus Caprifolium and subgenus Lonicera. Within subgenus Lonicera, sections Coeloxylosteum, Isoxylosteum, and Nintooa are nested within the paraphyletic section Isika. Section Nintooa may also be non-monophyletic. Our analysis of the genus Lonicera highlights instances of homoplasy in several morphological characters (e.g. hollow stems in subgenus Caprifolium and section Coeloxylosteum in subgenus Lonicera). Furthermore, our data indicate possible instances of hybridization in section Nintooa and biogeographic disjuctions between the Old and New Worlds (e.g. subsections Distegiae and Alpigenae).