Abstract With the disintegration of the traditionally circumscribed Scrophulariaceae, the phylogenetic placements of most genera formerly placed in that family have been resolved. However, the familial placement of the monotypic genus Mimulicalyx has not been included in any published molecular phylogenetic study. Here, we adopt a two-step approach to resolve the phylogenetic placement of Mimulicalyx using three datasets: (1) a 71 619 bp plastome alignment of Lamiales; (2) a dataset of six plastid DNA regions (atpB, matK, ndhF, rbcL, rps16 and trnL-trnF) for Phrymaceae; and (3) a dataset of the nuclear ribosomal internal and external transcribed spacer regions (nrITS, ETS) for Phrymaceae. Our analyses reveal that Mimulicalyx is a member of the tribe Mimuleae in Phrymaceae. Generic level phylogenetic relationships within Phrymaceae are further discussed, and a dichotomous key to the 15 genera currently recognized is provided.