Rhynchocyrtus Mendonça and Fernandes, 2007 is a monotypic genus of Entomobryidae, endemic to Brazil. Its placement within the Lepidocyrtinae and its systematic affinities with other members of the subfamily, especially with the subgenera of Lepidocyrtus Bourlet, 1839, have never been tested before. Here, we described the morphology and mitogenome of a new species of Rhynchocyrtus from the northeastern Brazilian Atlantic Forest (Rhynchocyrtus cleideae sp. nov. holotype female deposited in CC/UFRN: Brazil, Rio Grande do Norte State, Natal municipality), depicting for the first time the dorsal trunk chaetal pattern, homology and body pseudopores distribution for the genus. The new species description provided further data which we used to update the genus diagnosis, following the current standards used for other Entomobryidae. We also evaluated the phylogenetic placement of the genus within Lepidocyrtinae, testing its affinities with different subgenera of Lepidocyrtus. Our results point to Rhynchocyrtus as an ingroup of Neotropical Setogaster Salmon, 1951 subgenus, and not related to Cinctocyrtus Yoshii and Suhardjono, 1989 as previously suspected. Setogaster is likely a paraphyletic taxon, suggesting that some features currently used to separate Lepidocyrtus subgenera do not hold phylogenetic signal, and should be reevaluated. We discuss the problematic systematics of Lepidocyrtinae and reinforce the usefulness of some alternative morphological traits to better define its subgroups, based on the current knowledge of the group.