Partial sequences of the large subunit (LSU) and small subunit (SSU) of the ribosomal DNA of fucalean algae (Phaeophyceae) from the northern and the southern hemispheres, as well as from other brown algal genera such as Durvillaea, were analysed and compared with available morphological data. Combined SSU+LSU sequence data appear to be suitable for inferring phylogenetic relationships within the Fucales. Results suggest that Durvillaea and Notheia should be included in the Fucales and that the paraphyletic Cystoseiraceae be merged into a large family, Sargassaceae Kützing emend. De Toni. The genus Axillariella, the taxonomic position of which was uncertain, clearly belongs to the Sargassaceae. At present, at least seven families are recognized in the order Fucales: Durvillaeaceae, Seirococcaceae, Notheiaceae, Sargassaceae, Himanthaliaceae, Hormosiraceae and Fucaceae. More investigations are needed to assess whether Xiphophora should be placed in its own family.