Spongospora nasturtii is a plasmodiophorid pathogen of watercress (Rorippa nasturtium-aquaticum), causing crook root disease. In the past, some authors have considered the plasmodiophorids as protists, and others have considered them as true fungi. This study was performed with the aims of elucidating both the relationship of S. nasturtii to other plasmodiophorids, and also the placement of the plasmodiophorids as a group when compared to other organisms. Analysis of partial 18S ribosomal DNA sequences of a range of plasmodiophorids by phylogenetic techniques including parsimony, neighbour-joining, and principal co-ordinate analysis, indicated that there was a close relationship between S. nasturtii, S. subterranea and Plasmodiophora brassicae. However, analyses incorporating 1.2 kb of 18S rDNA sequence from S. subterranea cast doubt over the long-held view that S. subterranea and S. nasturtii are more closely related to each other than to other genera of plasmodiophorids. Consideration of the entire 18S rDNA of both S. nasturtii and P. brassicae showed that they are not closely related to a range of protists and true fungi examined.