Trichocoleopsis S. Okamura and Neotrichocolea S. Hatt. are two water saccate liverwort genera endemic to East Asia whose systematic positions have been controversial. To address their phylogenetic positions and relationships within liverworts, two data sets were analyzed using maximum parsimony and maximum likelihood methods: (1) four genes (psbA, rps4, 26S, and nad5) of 57 taxa, and (2) nine genes (chloroplast small subunit [SSU], large subunit [LSU], atpB, rbcL, psbA, and rps4; nuclear ribosomal 18S and 26S; mitochondrial nad5) of 24 taxa. All of our analyses suggested the sister relationship between Trichocoleopsis and Neotrichocolea, which is also supported by morphological characters, such as a lobed leaf with ciliate margins, water sacs, coelocaules, and interior capsule wall cells with thin walls. Traditional classifications usually considered Trichocoleopsis and Neotrichocolea as members of Lepidolaenaceae or Trichocoleaceae, whereas our results strongly suggested that the Trichocoleopsis–Neotrichocolea clade allied with Ptilidiaceae, which is supported by the similar ciliate and lobed leaves. However, considering many differences between them, such as in the perianth, sporeling type, water sacs, and rhizoids, we support a family rank for the Neotrichocoleaceae, containing Trichocoleopsis and Neotrichocolea, as previously suggested by Inoue in 1974.