Abstract: Ciliates in the order Metopida exhibit a global distribution and play essential roles as consumers of and common hosts to prokaryotes in both hypoxic and anoxic environments. Based on detailed morphological and morphometric data of Metopus es and Brachonella contorta, type species of two common and relatively species-rich metopid genera, we investigate the morphogenesis, and molecular phylogeny of each, and analyze the secondary structure of the V9 region of their 18S rRNA gene sequences. The new findings include: (1) These two species present two different stomatogenetic modes, which are stable within their respective genera and each can be regarded as a reliable generic feature for differentiation. (2) Both species share the same outcome regarding the parental oral apparatus, i.e., the old paroral membrane and adoral zone of membranelles are entirely reorganized in situ in the proter. (3) The paroral membrane is diplostichomonadal in the examined isolates, a feature which has long been overlooked and may be enigmatically present in other previously described populations. As concerns their phylogeny, the clear delineation of each species is supported by the high conservation of SSU rRNA gene sequences, and the close phylogenetic clustering, of different populations of each species from geographically distant localities. In agreement with previous phylogenetic studies, the MeBr clade (Metopus, including M. es and marine/brackish Metopus members, and all Brachonella species) is recovered repeatedly with moderate to high support.