In molecular phylogenetic studies, Lophopyxidaceae and Putranjivaceae are well supported as sisters in the large rosid order Malpighiales. As the floral structure of both families is poorly known and the two families have never been compared, the present comparative study was carried out, as part of a larger project on the comparative floral structure of Malpighiales, using microtome section series and scanning electron microscopy (SEM) studies. Similar to other angiosperm clades, it appears that the structure of the ovules is a strong marker for suprafamilial relationships in Malpighiales. Both families have two collateral pendant antitropous ovules per carpel associated with obturators (as in some Euphorbiaceae s.l., to which Putranjivaceae belonged in earlier classifications). However, in contrast with Euphorbiaceae s.l., the ovules are not crassinucellar, but either incompletely tenuinucellar or only weakly crassinucellar with a long and conspicuously slender nucellus and an endothelium, and do not have a nucellar beak, but a normal micropyle, features they share with families other than Euphorbiaceae s.l. among Malpighiales. Other shared features of the two families include the following. The outer sepals tend to be smaller than the inner ones and the sepals do not protect the gynoecium in older buds. Sepals of some taxa have a single vascular trace. A short zone of synsepaly tends to be present. Stamens tend to be antesepalous in haplostemonous flowers. A short gynophore is present. The synascidiate zone extends up to above the placenta, but is restricted to the ovary in taxa with more than one carpel. The micropyle is formed by the inner integument. The ventral carpel slits extend down into the synascidiate zone as postgenitally fused furrows. The carpels have a broad dorsal band of vascular bundles in the style. The overall floral structure of the two families corroborates their sister position well and does not support the earlier association of Putranjivaceae with Euphorbiaceae s.l. or of Lophopyxidaceae with Geraniales–Sapindales–Celastrales, which rely on shared superficial floral similarities. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172, 404–448.