Abstract: Cyrtophorians are a diverse and ecologically important group of protists, playing multiple roles in aquatic ecosystems. However, studies on the subclass Cyrtophoria remain limited, resulting in persistent confusion regarding their taxonomy, phylogeny and distribution. Three cyrtophorians isolated from the Yangtze Estuary, namely Monochilodonella sinica gen. et sp. nov., Chlamydonella foissneri sp. nov. and Gastronauta derouxi Blatterer & Foissner, 1992, were investigated using an integrative morpho-molecular approach. Monochilodonella sinica gen. et sp. nov. possesses a single circumoral kinety, which indicates that it represents a new lineage of Chilodonellidae. Both the secondary structure of the nuclear SSU rRNA molecule and the phylogenetic analyses place this new genus within Chilodonellidae, closely related to Pseudochilodonopsis. Chlamydonella foissneri sp. nov. clusters with Chlamydonellopsis species rather than its congeners, rendering both Chlamydonella and Chlamydonellopsis non-monophyletic. After briefly reviewing the family Chilodonellidae, we propose a hypothetical evolutionary trajectory for the family Chilodonellidae based on both morphological and molecular data. Furthermore, illustrated identification keys are provided for the genera of Chilodonellidae and for species of Chlamydonella.