The major goal of this study was to re-analyse a published molecular dataset based on ITS and matK sequences of the genus Ceratophyllum (Ceratophyllaceae) within a cladistic framework, operating only with rooted trees. The problem is lack of an identifiable suitable outgroup to Ceratophyllum. We show different ways to root trees and thus resolve the sister group relationships within this genus. We root the trees using an all zero outgroup or a combination of exemplar taxa from among monocots (Acorus), eudcots (Ranunculus) and Chloranthus. Ceratophyllum echinatum was consistently strongly supported as sister to all of the remaining taxa of the genus. This observation is congruent with the earlier results of Les who noted the uniqueness of C. echinatum in a series of comprehensive morphological and biosystematic studies. We, here, transfer C. echinatum to a new and presumably monotypic genus Fassettia Mavrodiev. The exact taxonomic circumscription of Fassettia requires further investigation.