Trigonia cipoensis has a trizonate ovule primordium. The mature ovule is anatropous, bitegmic and tenuinucellate. Both integuments are of dermal origin; the inner integument is strongly multiplicative, especially after fertilisation. The mature seed is densely covered by cottony testal hairs. Of the inner integument the outer layer develops into a lignified, fibrous exotegmen, whereas the inner layer is tanniniferous. Endosperm formation is initially nuclear, the tissue later becoming cellular throughout. Ovule and seed structure indicates a relationship with the Linales and not with the Polygalales with which the family Trigoniaceae is ususally associated.