The phylogeny of Alisma (Alismataceae), a genus of approximately nine species of aquatic plants mainly distributed in the Northern Hemisphere, was reconstructed with parsimony analysis on RAPD data and sequences of the nuclear ITS and chloroplast trnL regions, and with MDS on RAPD data. Separate analyses were performed on each data set. Butomus umbellatus was used as outgroup in the analysis of sequence data, and Luronium and Baldellia in the analyses of RAPD data. Among diploid Alisma, two major groups were found: (i) the gramineum group consisting of A. gramineum and A. wahlenbergii, and (ii) the plantago-aquatica group with A. plantago-aquatica, A. orientale, A. subcordatum, A. juzepczukii and A. "bottnicum". Taxa within the groups were poorly separated. The Baltic endemics A. wahlenbergii, A. juzepczukii and A. "bottnicum" have probably originated relatively recently from local populations of A. gramineum (i.e. A. wahlenbergii) and A. plantago-aquatica (i.e. A. juzepczukii and A. "bottnicum"). The exact origin of the polyploid taxa, i.e. A. lanceolatum, A. triviale, A. canaliculatum and A. rariflorum, is still unclear.