Members of the liverwort family Fossombroniaceae are typically identified by the distinct ornamentation patterns on their spores. We have tested the hypothesis for Australian Fossombronia that using spore morphology is sufficient to identify species based on a monophyly criterion applied to a molecular phylogeny. We used the chloroplast markers rps4 and trnL-F and the nuclear internal transcribed spacer (ITS) region to develop a phylogeny based on multiple accessions per putative morphospecies. Whilst the relationship between species had little support, the results did strongly support seven out of the eight species groupings based on spore morphology.