The Internal Transcribed Spacer (ITS1) has been used in many molecular studies on closely allied organisms. Based on its high variability it is said to be useless for obtaining phylogenies at higher taxonimical levels. However, the secondary structure of the ITS1 region is more conserved than the primary structure (i.e., the sequence itself) and is therefore a useful tool for optimizing alignments. A general secondary structure of ITS1 for Boraginales is proposed (a stem-loop with four major helices), and some derivations found in the subclades are discussed. Helices II and III are short and conserved, while helices I and IV are comparably long and have high variability. Behind helix III the motif AAGGAA is found that is probably conserved in all Asteridae, and it is said to have a key function during the splicing process. Considering the information from secondary structure increases the number of structural characters which can be used for phylogenetic studies in a traditional way. Information inferred from the secondary structure enables us to reconstruct well-resolved phylogenetic trees at higher taxonomic levels. In our application of secondary structure in the Boraginales we could demonstrate the polyphyly of Boraginaceae s.l.: Boraginaceae s.str. are the sistergroup of a clade formed by Hydrophyllaceae s.str., Cordiaceae, Ehretiaceae, Heliotropiaceae, and Lennoaceae. The last four taxa constitute a monophyletic group, which is the sistergroup of Hydrophyllaceae s.str. Parasitic Lennoaceae are probably closely allied to Ehretiaceae. These hypotheses are supported by numerous morphological features.

Key words: Boraginales, ITS1, phylogeny, secondary structure