Anacardiaceae and Burseraceae are traditionally distinguished by the number of ovules (1 vs. 2) per locule and the direction of ovule curvature (syntropous vs. antitropous). Recent molecular phylogenetic studies have shown that these families are sister groups in Sapindales after having been separated in different orders for a long time. We present a comparative morphological study of the flower structure in both families. The major clades, usually supported in molecular phylogenetic analyses, are well supported by floral structure. In Anacardiaceae, there is a tendency to gynoecium reduction to a single fertile carpel (particularly in Anacardioideae). The single ovule has a long and unusually differentiated funicle, which connects with the stylar pollen tube transmitting tract in all representatives studied. In Anacardiaceae-Spondiadoideae, there is a tendency to form an extensive synascidiate zone, with a massive remnant of the floral apex in the centre; these features are also present in Beiselia (Burseraceae) and Kirkiaceae (sister to Anacardiaceae plus Burseraceae) and may represent a synapomorphy or apomorphic tendency for the three families. In core Burseraceae, gynoecium structure is much less diverse than in Anacardiaceae and has probably retained more plesiomorphies. Differences in proportions of parts of the ovules in Anacardiaceae and Burseraceae are linked with the different direction of ovule curvature.