According to phylogenetic analyses of nrDNA ITS1 and ITS2 sequences (including the 5.8S unit) the Neotropical Plagiochila moritziana, P. rutilans var. rutilans, P. rutilans var. standleyi, P. trichostoma (= P. permista, syn. nov.), and P. subtrinitensis form a monophyletic lineage and are placed in P. sect. Rutilantes; all five taxa lack a ca 20 base pair sequence that is present in all the taxa of the other Plagiochila sections investigated. The Central American P. subtrinitensis is treated as a synonym of the Hawaiian endemic P. deflexa. Plagiochila moritziana is excluded from sect. Fuscoluteae and reduced to a variety of P. rutilans; P. sect. Permistae is treated as a synonym of P. sect. Rutilantes. The sporophytes of P. trichostoma and P. deflexa are described for the first time. Fresh material of P. rutilans var. moritziana exhibits a distinct odor of peppermint caused by the presence of several menthane monoterpenoids, principally pulegone. The Central American P. rutilans var. standleyi is reported from Ecuador, new to South America. Lectotypes are designated for P. rutilans var. moritziana, P. subtrinitensis, and P. trichostoma.
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