Ciliated protists are unicellular eukaryotes that play important roles in aquatic ecosystems. One of the major tasks of ciliate taxonomy is to re-evaluate the systematic confusing taxa using modern methods. In the present study, two peniculid ciliates, Maritujacf. caudata and Disematostoma minor collected from east China, were studied using a multi-method approach. New morphological observations supplied additional information for species identification and systematic revision of the order Peniculida. The small subunit ribosomal RNA gene sequences of M. cf.caudata, D. minor, and Frontonia terricola were characterized for the first time and provided newinsights into the phylogeny of Peniculida. The family Stokesiidae Roque, 1961, was expanded to include the genera Disematostoma and Marituja in addition to its type genus Stokesia, since the three genera formed a well-supported clade in the phylogenetic analyses. The diagnosis of Stokesiidae was improved to include the newly recognized synapomorphies, i.e., barren kinetosomes on the dorsal side, a ciliated dorsal suture, and the somatic ciliature that can be recognized as transversely oriented circles. Additionally, the systematic relationships of the genera and families of Peniculida were hypothesized. We argue that more diversified morphological features should be considered when assessing diagnostic traits for ciliate taxa
during systematic revisions.