Phylogenetic analyses of representative species from the five genera of Winteraceae (Drimys Pseudowintera Takhtajania Tasmannia and Zygogynum s.l.) were performed using ITS nuclear sequences and a combined data-set of ITS + psbA-trnH + rpS16 sequences (sampling of 30 and 15 species respectively). Indel informativity using simple gap coding or gaps as a fifth character was examined in both data-sets. Parsimony and Bayesian analyses support the monophyly of Drimys Tasmannia and Zygogynum s.l. but do not support the monophyly of Belliolum Zygogynum s.s. and Bubbia. Within Drimys the combined data-set recovers two subclades. Divergence time estimates suggest that the splitting between Drimys and its sister clade (Pseudowintera + Zygogynum s.l.) occurred around the end of the Cretaceous; in contrast the divergence between the two subclades within Drimys is more recent (15.5–18.5 MY) and coincides in time with the Andean uplift. Estimates suggest that the earliest divergences within Winteraceae could have predated the first events of Gondwana fragmentation.