Background and aims – As a result of the description of many new species, reanalyses of type material, and information becoming available on valve morphogenesis in small araphid diatoms lacking a rimoportulae, the existing classification scheme at the genus level needs revision. Because morphological information has increased manyfold since the system provided by Williams & Round (1987), it may now be possible to find distinguishing characters in order to produce a more stable and useful framework, encompassing a morphogenetic perspective, which could then guide the placement of newly discovered taxa. This new framework could also be used to help assess the molecular information generated for the group, based on which many new genera are being erected, but perhaps without proper pondering of morphological data.
 Methods – A thorough review was made of available published information on the ultrastructure of small-celled araphid diatoms lacking rimoportulae. In addition, image databases were searched, and new light and scanning electron microscopical observations made of some hitherto undescribed species.
 Key results and conclusions – We provide a table of putative distinguishing features for nine genera (Nanofrustulum, Opephora, Pseudostaurosira, Pseudostaurosiropsis, Punctastriata, Sarcophagodes, Stauroforma, Staurosira and Staurosirella), together with a discussion on their value for discriminating these small diatoms using a morphogenetic perspective. Based on our findings, we amend the genus Pseudostaurosira, establishing wide and short vimines as its most characteristic feature. We use our system in describing a new species from Bolivia, which we place in Nanofrustulum based on its quasifract copulae, the distinguishing trait of the genus. The new species is distinguished from its congeners by its heteropolar valves, apical pore field features, and the multiseriate areolae. We also examine the three genera Popovskayella, Gedaniella, and Serratifera, the latter two recently erected based on molecular information. Since none of these latter genera pass the morphogenetic evaluation we think is essential, we place them in synonymy with other genera and provide the consequent nomenclatural changes. Finally, we make several new combinations in Nanofrustulum, Pseudostaurosira, Sarcophagodes and Staurosirella.
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