This study seeks to determine the phylogenetic position of the diatom genus Rhoicosphenia. Currently, four hypotheses based on the morphology of the siliceous valve and its various ultrastructural components, sexual reproduction, and chloroplasts have been proposed. Two previous morphological studies have tentatively placed Rhoicosphenia near members of the Achnanthidiaceae and Gomphonemataceae, and no molecular studies have been completed. The position of Rhoicosphenia as sister to 'monoraphid' diatoms is problematic due to the apparent non-monophyly of that group, so hypotheses of 'monoraphid' monophyly are also tested. Using an analysis of morphological and cytological features, as well as sequences from three genes, SSU, LSU, and rbcL, recovered from several freshwater Rhoicosphenia populations that have similar morphology to Rhoicosphenia abbreviata (Agardh) Lange-Bertalot, we have analyzed the phylogenetic position of Rhoicosphenia in the context of raphid diatoms. Further, we have used topology testing to determine the statistical likelihoods of these relationships. The hypothesis that Rhoicosphenia is a member of the Achnanthidiaceae cannot be rejected, while the hypothesis that it is a member of the Gomphonemataceae can be rejected. In our analyses, members of the Achnanthidiaceae are basal to Rhoicosphenia, and Rhoicosphenia is basal to the Cymbellales, or a basal member of the Cymbellales, which includes the Gomphonemataceae. Hypothesis testing rejects the monophyly of 'monoraphid' diatoms.