The chemical composition of sporopollenin has long been elusive due to its unusual chemical stability, insolubility and resistance to degradation by enzymes and strong chemical reagents. It was once thought to consist of polymerised carotenoids but the application of more detailed analytical methods since the 1980s has shown that this is not correct. Analyses have revealed a complex biopolymer, containing mainly long-chain fatty acids, phenylpropanoids, phenolics and traces of carotenoids in a random co-polymer. It is likely that sporopollenin derives from several precursors that are chemically cross-linked to form a rigid structure. There is also good evidence that the chemical composition of sporopollenin is not the same in all plants, indicating it is a class of compounds rather than having one constant structure.
In 2019, thioacidolysis degradation and solid-state NMR was used to determine the molecular structure of pitch pine sporopollenin, finding it primarily composed of polyvinyl alcohol units alongside other aliphatic monomers, all crosslinked through a series of acetal linkages. Its complex and heterogeneous chemical structure give some protection from the biodegradative enzymes of bacteria, fungi and animals. Some aromatic structures based on p-coumarate and naringenin were also identified within the sporopollenin polymer. These can absorb ultraviolet light and thus prevent it penetrating further into the spore. This has relevance to the role of pollen and spores in transporting and dispersing the gametes of plants. The DNA of the gametes is readily damaged by the ultraviolet component of daylight. Sporopollenin thus provides some protection from this damage as well as a physically robust container.
Analysis of sporopollenin from the clubmoss Lycopodium in the late 1980s have shown distinct structural differences from that of flowering plants. In 2020, more detailed analysis of sporopollenin from Lycopodium clavatum provided more structural information. It showed a complete lack of aromatic structures and the presence of a macrocyclic backbone of polyhydroxylated tetraketide-like monomers with pseudo-aromatic 2-pyrone rings. These were crosslinked to a poly(hydroxy acid) chain by ether linkages to form the polymer.