A phylogenetic analysis of Hydrocharitaceae was conducted using data from the internal transcribed spacers (ITS-1;2) of the nuclear ribosomal genes, the chloroplast gene IrbcL and the flanking introns of the chloroplast matK gene. The aquatic, monocotyledonous Hydrocharitaceae consist of 17 genera which are highly variable in habitat, pollination and morphology. Numerous convergences and reduced vegetative and reproductive structures make it difficult to interpret morphological characters for phylogenetic analysis. Our combined data set showed high congruency with results published previously using rbcL data alone, or a combination of rbcL and matK (coding region) data. The combined molecular data consistently show a monophyletic origin for the family. Other results include the monophyly of seagrass genera (Enhalus, Halophila and Thalassia), a possible sister group relationship of Najadaceae and Hydrocharitaceae, and several well-supported monophyletic clades within the family. Currently, morphological and developmental characters within the Hydrocharitaceae are being investigated to supplement the molecular data for further investigation of relationships.

Key words: Hydrocharitaceae, ITS, matK, morphology, phylogeny, systematics