Trichodinids (Ciliophora: Peritrichida) are one of the most common parasitic ciliates which can cause serious diseases in aquaculture animals of both marine and freshwater environments. Therefore the study of these ciliates is necessary in order to prevent and control such diseases. Here we review the history of the taxonomy and phylogeny of the trichodinids. Under taxonomy, we introduce the parasitic positions and geographic distribution of trichodinids. Furthermore, we summarize a three-stage pylogenetic process based on morphological and molecular characters. Finally, we make some suggestions on the future study of the taxonomy and phylogeny of trichodinids.