Mesopedinella arctica, Daugbjerg a marine phytoflagellate, was recently described ultrastructurally and observed to possess characters common to the Pedinellales Zimmermann, Moestrup et Hällfors. To infer the phylogenetic position of this new genus within the Pedinellales, including all well-circumscribed genera, and to study relationships among the three orders in the Dictyochophyceae Silva, a cladistic analysis was performed on a data matrix of 33 ultrastructural characters. The Pedinellales proved to be monophyletic and Mesopedinella to be closely related to Pedinella hexacostata Wyssotzki. Pseudopedinella tricostata (Rouchijajnen) Thomsen, with three chloroplasts, was the most basal pedinellid suggesting that six chloroplasts is the advanced state. The heterotrophic pedinellids form a monophyletic group, suggesting that there was a single loss of chloroplasts within this cluster. Within the Dictyochophyceae, the silicoflagellate Dictyocha speculum Ehrenberg was the most divergent taxon. The cladistic analysis constitutes an independent hypothesis of phylogenetic relationships of the Dictyochophyceae to which reconstructions based on molecular data can be compared.