Species-level relationships within the pantropical, largely rainforest genus Cryptocarya R.Br (Lauraceae) and allied groups have long been problematic. Here, we utilise nuclear RPB2 and plastid trnL–trnF sequence data to reconstruct the phylogenetic relationships among Australian Cryptocarya species. We relate our findings to the previous two disparate attempts to resolve species-level relationships on the basis of traditional taxonomic tools. Our results showed that an early diversification gave rise to two lineages present in Australia and globally. The loss of cataphylls (bract-like leaves in seedlings) seems to be a derived state only found in the larger of these two clades. Ruminate cotyledons is another potentially informative character; however, it is highly likely that this condition arose through convergent or parallel evolution. Little or no molecular variation was observed between many species, which suggests recent diversification. Furthermore, the close relationships between species from two geographically disjunct centres of rainforest diversity within Australia suggests that loss of between-region connectivity is recent. A global revision of the group, incorporating molecular analyses and seedling and fruit morphology, is needed to untangle the complex evolutionary relationships within this genus.