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Within the angiosperm subclass Alismatidae (= superorder Alismatiflorae), contemporary taxonomists have often assigned the families Hydrocharitaceae and Najadaceae to different orders. The Najadaceae are presumably allied to a variety of aquatic families in the order Najadales, whereas the Hydrocharitaceae have been segregated as the order Hydrocharitales or placed within the order Alismatales. Analysis of DNA sequence data from the chloroplast gene rbcL, however, indicate that Najadaceae have a much closer phylogenetic relationship to Hydrocharitaceae than to families of the "Najadales" (Cymodoceaceae, Potamogetonaceae, Ruppiaceae, Scheuchzeriaceae, Zannichelliaceae, Zosteraceae). This association supports previous studies based upon examination of floral structure and seed coat anatomy. The rbcL sequence data also indicate that the Zosteraceae and Potamogetonaceae are closely related families. The rbcL sequence of Zostera is actually more similar to that of Potamogeton richardsonii than is the sequence of the latter to a congener, Potamogeton amplifolius. The marine, dioecious, hydrophilous genus Zostera has acquired a number of distinctive adaptations, but probably diverged relatively rapidly from freshwater Potamogetonaceae. Molecular data place Ruppiaceae as a sister group to the marine Cymodoceaceae and do not support the commonly accepted merger of Ruppiaceae and Potamogetonaceae.

Aquatic plants are notoriously difficult to study systematically due to convergent evolution and reductionary processes that result in confusing arrays of morphological features. Plant systematists have frequently focused their attention on the "water lilies," putative descendants of the most archaic angiosperms. Classification of these 10 plant genera varies from recognition of one to three orders containing three to six families. We have used DNA sequence analysis as a means of overcoming many problems inherent in morphologically based studies of the group. Phylogenetic analyses of sequence data obtained from a 1.2-kilobase portion of the chloroplast gene rbcL provide compelling evidence for the recognition of three distinct lineages of "water lily" plants. Molecular phylogenies including woody Magnoliidae sequences and sequences of these aquatic plants depict Ceratophyllum as an early diverging genus. Our results support hypotheses that most taxonomic concepts of the order Nymphaeales reflect polyphyletic groups and that the unusual genus Ceratophyllum represents descendants of some of the earliest angiosperms.