The aim of this work was to develop rigorous phylogenetic hypotheses for the mostly Australian species of Mimulus, Glossostigma, Peplidium, Microcarpaea and Elacholoma (Phrymaceae sensu Beardsley and Olmstead 2002), and to use the phylogeny to explore morphological patterns of evolution. Chloroplast trnL/F and nuclear ribosomal internal and external transcribed spacer sequence data were used to analyse phylogenetic relationships. The results of these analyses confirmed the following conclusions proposed in previous morphological analyses: (1) Glossostigma and Peplidium are supported as monophyletic groups, although support is weak for Peplidium; (2) Australian endemic Elacholoma, in the past of uncertain family placement, is embedded within the same clade as the former two genera despite its unique pair of terete stigmatic lobes; (3) a relatively recent dispersal event from Australia to Iraq and the Middle East for P. maritimum is inferred; (4) a reduction in stamen number from four to two has evolved independently several times in Glossostigma, Peplidium, Microcarpaea and Elacholoma; (5) a switch to an obligately autogamous breeding system has evolved several times independently in the group. New findings include the following: (1) Glossostigma, Peplidium, Microcarpaea and Elacholoma are derived from within Mimulus; (2) Mimulus prostratus is part of a clade that contains Elacholoma and Glossostigma, and this clade is not a part of the same clades as other Mimulus species in Australia; (3) there is some support for Microcarpaea being sister to a clade including Elacholoma, Mimulus prostratus, Glossostigma and Peplidium. The discovery that four mostly Australian genera are derived from within the mostly western North American genus Mimulus has important implications for generic assignments. Phylogenetic interpretations of additional morphological character transformations are discussed.