Small subunit ribosomal RNA genes of 12 ciliate morphospecies from seven genera (subclasses Oligotrichia and Choreotrichia), Parallelostrombidium, Pseudotontonia, Spirostrombidium, Spirotontonia, Tintinnopsis, Favella and Strombidium were sequenced. Phylogenetic trees, constructed using Bayesian inference, maximum likelihood, maximum parsimony, and after likelihood yielded essentially the same topology. The tail-less Laboea groups with the tail-bearing Spirotontonia and Pseudotontonia, challenging the diagnostic feature of the family Tontoniidae. The three Spirostrombidium species form a monophyletic group, supporting the separation of Spirostrombidium from the morphologically related genus Strombidium. Parallelostrombidium branches off basally to the Spirostrombidium clade, to some extent supporting Agatha's division of these two similar genera. Under the approximately unbiased (AU) test, topologies constrained for Strombidium monophyly were found not to be significantly worse (P > 0.05) than unconstrained topologies in which Strombidium conicum grouped with non-Strombidium species. Therefore, we can not refute the monophyly of Strombidium. Our analyses also support the previous reports that the genus Tintinnopsis is polyphyletic.