Phylogenetic relationships within the green algal class Cladophorophyceae were investigated. For 37 species, representing 18 genera, the sequences of the 5'-end of the large subunit rRNA were aligned and analysed. Ulva fasciata and Acrosiphonia spinescens (Ulvophyceae) were used as outgroup taxa. The final alignment consisted of 644 positions containing 208 parsimony-informative sites. The analysis showed three lineages within the Cladophorophyceae: Cladophora horii diverged first, followed by two main lineages. The first lineage includes some Cladophora species and genera with a reduced thallus architecture. The second lineage comprises siphonocladalean taxa (excluding part of Cladophoropsis and including some Cladophora species). From this perspective the Siphonocladales forms a monophyletic group, the Cladophorales remaining paraphyletic.