We investigated species in the family Phyllophoraceae from Peru using sequences of the plastid rbcL sequences and morphological examination. Here we describe Acletoa tarazonae gen. & sp. nov., characterized by the presence of secondary medullary cells around cystocarps, gonimoblast initials that are downwardly and upwardly directed, and a linear arrangement of gonimoblast filaments on medullary cells. Acletoa tarazonae consistently formed a clade with Ahnfeltiopsis vermicularis and Chilean Gymnogongrus sp., and this clade was distinct from other genera in the Phyllophoraceae in the rbcL phylogeny. We also describe a new species of the Phyllophoraceae, Gymnogongrus caespitosus sp. nov., from northern Peru, characterized by a semirigid and flattened thallus, narrow branches, absence of hair cells, and cystocarps immersed in a single cavity. Ahnfeltiopsis concinna was not distinct from Ahnfeltiopsis durvillei, and consistently grouped in the genus Gymnogongrus sensu stricto in the rbcL phylogeny. A new combination of Gymnogongrus durvillei comb. nov. was made on the basis of A. durvillei, and A. concinna was merged with G. durvillei.