Molecular systematics has clarified the limits of Loganiaceae (Gentianales), the tribal circumscriptions and the phylogenetic relationships within the family. Loganieae includes seven genera; however, generic boundaries remain untested and intergeneric relationships are largely unknown. The chloroplast intron petD and the nuclear ribosomal ETS were sequenced for 37 ingroup accessions, including all genera of Loganieae, to infer generic and infrageneric boundaries and intergeneric relationships within the tribe. Maximum parsimony and Bayesian analyses resolved several strongly supported clades. Mitreola s. str. was placed sister to the rest of Loganieae. The south-western Australian endemic, Mitreola minima B.J.Conn, was placed sister to Mitrasacme, Schizacme and Phyllangium, rendering Mitreola polyphyletic. Mitrasacme, Logania section Logania and L. section Stomandra were each strongly supported as monophyletic, but there was no support for the monophyly of Logania. Geniostoma was paraphyletic with respect to a monophyletic Labordia. It is here recommended that Mitreola minima be afforded generic status and that the three species of Labordia used in the present study be reduced to synonymy of Geniostoma. Additional sampling is needed to clarify the relationship between Logania section Logania and L. section Stomandra and to increase support for intergeneric relationships in Loganieae.