River banks are home to unusual, morphologically highly specialized bryophyte taxa, which have been little studied. Here we describe a novel rheophilous and epiphyllous liverwort from Ecuador, Cololejeunea stotleriana, with many unusual morphological features such as robust stem, flat, triangular lobules, large rhizoids fields that are not produced near the base of each leaf, superfertility and clustered gynoecia. Because of its puzzling morphology, we used two regions of the chloroplast genome (trnK-H, trnL-F) to explore the systematic affinity of this new species. It turned out to be the second member of the subgenus Chlorolejeunea and the first record of this Asiatic subgenus from the New World. The species was found growing associated with the rare mosses Fissidens hydropogon and Lepidopilum caviusculum, both only known from their type specimens collected 150 years ago. The unusual morphological traits of Cololejeunea stotleriana are interpreted as adaptations to the harsh rheophilous and epiphyllous environment. The deviating morphology of the new species indicates that extreme morphological transformations can obscure the phylogenetic signal present in morphological data.