We present four genera of bipolar centric diatoms with linking structures located on the valve face: Rutilaria (including two new species from the Cretaceous), Spinivinculum, Pseudorutilaria and Kisseleviella, which are commonly classified in the family Rutilariaceae. Functional comparison of their linking structures and modes of chain formation shows considerable diversity and does not support a close phylogenetic relationship among them. In order to reflect the probable phylogeny of this group, the Rutilariaceae is retained as a monotypic family, while Kisseleviella is transferred to the Cymatosiraceae. Rymariopsis gen. nov. is proposed as a possible link between the Hemiaulaceae and the Rutilariaceae. Based on the comparison of the stratigraphic ranges of these taxa with other diatoms, we explore the possibility of a close phylogenetic relationship between bipolar centric diatoms with centrally located linking structures and pennate diatoms, as suggested by recent molecular phylogenies. As a consequence, the Rutilariaceae is suggested as a possible sister taxon of the pennate diatoms.