SummaryAndersson, L. & Andersson, S.: A molecular phylogeny of Tropaeolaceae and its systematic implications. – Taxon 49: 721–736. 2000. – ISSN 0040‐0262.Relationships among 35 species of Tropaeolaceae are estimated based on nucleotide sequence variation in plastid DNA (the rbcL gene and the rps16 intron) and nuclear ribosomal DNA (the ITS1–5.8S‐ITS2 tandem repeat). Tropaeolum becomes paraphyletic when Magallana and Trophaeastrum are segregated; therefore, Magallana and Trophaeastrum should be reduced to synonyms of Tropaeolum. The two new combinations Tropaeolum porifolium (Cav.) L.Andersson & S.Andersson and T. trialatum (Suess.) L. Andersson & S. Andersson are made. Further, although most of the sections of Tropaeolum that were recognised in Sparre and Andersson's monograph are monophyletic, only two entities can be distinguished that are both monophyletic and morphologically diagnosable. Therefore, the genus Tropaeolum should be subdivided into two sections, T. sect. Tropaeolum and T. sect. Chilensia. Tropaeolum sect. Tropaeolum should include the formerly recognised sections Bicolora, Dipetala, Mucoronata, Schizotrophaeum, Serratociliata, Tropaeolum, and Umbellata. Tropaeolum sect. Chilensia should include the formerly recognised genera Magallana and Trophaeastrum, and the formerly recognised T. sect. Chymocarpus.