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Pennantia, which comprises four species distributed in Australasia, was the subject of a monographic taxonomic treatment based on morphological characters in 2002. When this genus has been included in molecular phylogenies, it has usually been represented by a single species, P. corymbosa J.R.Forst. & G.Forst., or occasionally also by P. cunninghamii Miers. This study presents the first dated phylogenetic analysis encompassing all species of the genus Pennantia and using chloroplast DNA. The nuclear ribosomal 18S-26S repeat region is also investigated, using a chimeric reference sequence against which reads not mapping to the chloroplast genome were aligned. This mapping of off-target reads proved valuable in exploiting otherwise discarded data, but with rather variable success. The trees based on chloroplast DNA and the nuclear markers are congruent but the relationships among the members of the latter are less strongly supported overall, certainly due to the presence of ambiguous characters in the alignment resulting from low coverage. The dated chloroplast DNA phylogeny suggests that Pennantia has diversified within the last 20 My, with the lineages represented by P. baylisiana (W.R.B.Oliv.) G.T.S.Baylis, P. endlicheri Reissek and P. corymbosa diversifying within the last 9 My. The analyses presented here also confirm previous molecular work based on the nuclear internal transcribed spacer region showing that P. baylisiana and P. endlicheri, which were sometimes considered synonyms, are not sister taxa and therefore support their recognition as distinct species.