Structural characterization of naturally occurring polyisoprenes was carried out to solve the mystery of natural rubber (NR), such as the biosynthesis mechanism of rubber formation, the origin of outstanding properties of NR and the role of rubber in rubber trees. The NMR analysis, based on terpenes and polyprenols as models, disclosed the structure of both terminal groups of rubber chain. Structural evidence indicated that the biosynthesis of rubbers from Lactarius mushroom and leaves of high plants starts from trans, trans-farnesyl diphosphate or trans, trans, trans-geranylgeranyl diphosphate and terminates by dephosphorylation to form a hydroxyl terminal group. The biosynthesis of NR was presumed to start from unidentified initiating species containing two trans-isoprene units and peptide group and to terminate forming a phospholipid terminal group. The initiating group of NR associated with proteins formed branch points, which can be decomposed by enzymatic deproteinization. The branch points formed by phospholipid group were decomposed by transesterification with sodium methoxide. Rapid crystallization of NR was explained by the presence of mixed fatty acids synergistically with linked fatty acids, which were included in phospholipid. Saturated fatty acids linked to rubber chain induced crystallization, while mixed unsaturated fatty acids acted as plasticizer and accelerated the crystallization rate. This was confirmed by the preparation of model cis-polyisoprene grafted with stearic acid. The green strength of NR decreased to the same level as synthetic cis-polyisoprene after transesterification, indicating the effect of branching formed by the phospholipid terminal group and fatty acids in NR. The role of NR in Hevea trees was analyzed using NR from Hevea trees never tapped before. The formation of hard gel and oxidative degradation during the storage of NR in Hevea trees suggested that NR acted as a radical scavenger to remove hydroperoxide.