Different geological periods have witnessed the origin and differential diversification of various plant lineages on the Earth from Bryophytes, Ferns and allies, Gymnosperms, and Angiosperms. For example, Gymnosperms became dominant during the Mesozoic era but have declined since the emergence of angiosperms. About 1000 species of gymnosperms exist and are mostly limited to cold, dry, and high elevational or latitudinal areas. Angiosperms have radiated explosively since the early Paleocene with over 250,000 species. The differential diversification of various lineages has been associated with innovative traits such as the vascular system in vascular plants, seed in seed plants, and flower and fruit in angiosperms. Morphological and genetic integration may have existed during the evolution of the innovations but have not been explored in a comprehensive way. Therefore, the pleiotropic relationships among traits may offer an alternative to explain the differential diversification of major lineages of plants. Furthermore, some trait(s) may also be used to predict how plants perform with global environmental changes. Lignin is an important organic compound for plant cell integrity and function, and may be pleiotropically linked with the evolution of derived traits in bryophytes, ferns, gymnosperms, and angiosperms. The evolutionary pattern of lignification may provide new insights into differential diversification of plant lineages and is likely to be informative in predicting the impact of climatic change on composition and function of ecosystems. The existing lignin data show a continuing downward trend from the early plants to angiosperms, while genetic and biochemical analyses indicate that lignification and the production of flavonoids are negatively related. The negative relationship suggests a continuing upward trend of the production of flavonoids in plants, which are associated with plant development, survival, and biomass production. Both lignification and the production of flavonoids are parts of the phenylpropanoid biochemical pathway starting from the amino acid phenylalanine and both take a large amount of energy to produce. Therefore, there exists an ecological trade-off between the two competing pathways. Meanwhile, the genes involved in the two pathways are conservative or evolutionarily constrained, which is shown by the different levels of lignin in bryophytes, ferns, gymnosperms, and angiosperms. The declining amount of lignin has left more energy for biomass production via cell division and growth, and subsequently higher genetic variation, better survival, and greater diversification. In an ecosystem with plants of differential levels of lignin production, the ones with less energy for lignin may complete better than the ones with more energy for lignin production. However, in certain ecosystems (e.g., boreal forests), plants of a higher amount of lignin are more competitive (e.g., conifers). Therefore, I hypothesize that the evolutionary constraint and ecological trade-off of the phenylpropanoid pathway may be linked with the differential diversification of plants in the past, present, and future. A large amount of data from lignification, production of flavonoids, and genomics/proteomics of various plants in nature and controlled environment are needed to test the idea. The theory may have far-reaching implications for ecological and evolutionary studies and for conservation and climatic changes.