Members of the orchid family occupy many germination niches, in terrestrial, epiphytic and epilithic environments. How orchid seeds attach to their substrate and survive after dispersal is largely unknown. C-lignin is a recently discovered specialized lignin, found in seed coats of some plants, including orchid species, but its functional and biological significance is obscure. We studied seed coat ontogenesis in three species (Neuwiedia veratrifolia, Cypripedium formosanum and Phalaenopsis aphrodite) that represent basal and advanced branches in orchid phylogeny and divergent life forms. From each species, controlled pollination yielded several stages of seed development, from which seed coats (testa) were isolated and analysed by ATR-FT-IR spectroscopy. The use of the ATR set-up ensured that the chemical information originated only from the integral outer seed surface layers. The FT-IR bands of C-lignin are presented here for the first time, and distinguished from bands of G/S-lignin. In the seed coats, C-lignin developed after G/S-lignin in N. veratrifolia and C. formosanum, while only G/S-lignin developed in P. aphrodite. We discuss C-lignin properties and possible function in relation to seed coat properties. The species differed with respect to sequence and amounts of deposition, not only of lignins but also lipids, resulting in differences in mature seed coat compositions. Thus we revealed an unexpected and marked diversity among orchids with respect to seed surface chemistry, with possible implications for seed and germination ecology.