The colonisation intensity and composition of the mycorrhizal community in the aquatic plants Lobelia dortmanna and Littorella uniflora were studied. The mycorrhizal fungi were characterised by fungal specific nested PCR and sequencing using the 5'-end of the LSU rDNA as target. For this, primers for the clade of Acaulospora, the clade including Glomus mosseae and G. intraradices and the clade containing G. etunicatum and G. claroideum were used. The nested PCR products were screened for different sequence types using single stranded conformation polymorphism (SSCP) and representatives for each type were sequenced. A phylogenctic analysis of the sequences showed two phylotypes of Acaulospora, one phylotype within the clade of G. etunicatum/G. claroideum and five within the G. mosseael G. intraradices clade. The colonisation intensity was comparable to that seen in typical grassland vegetation. The neutral lipid fatty acid 16: 1omega5 was seen to be indicative of mycorrhizal colonisation with concentrations up to 35 nmol mg(-1) root DW, which indicates that the fungi are active.