Andean South America, including the adjacent lowland environments, can be evaluated in reference to the patterns and processes that characterize plant diversity, evolution, and distribution. Although its ecological complexity is bewildering and the evolutionary and geological history is convoluted and poorly understood, progress can be made by testing the relationship of known processes and paleoevents to patterns of diversification and distribution.Plant diversity patterns can be quantified and mapped in order to permit the study of linkages to environmental parameters and to past speciation and extinction processes. Such studies show the importance of dispersal barriers and long altitudinal gradients for the evolution of Andean plants. Phylogenetic studies allow for the tying of these processes to the timing of connections from the Andes to adjacent tropical forests, grasslands, and deserts, to other highlands in South America, or to other continents. They can also reveal temporal relationships among a variety of plant lineages, allowing for the identification of basal groups, of paleoendemics, and of the recently derived neoendemics. The special places in South America that have high representation of these restricted-range taxa can be better understood as a result. In the Andean context, these are often located in isolated habitat islands, with moisture regimes ranging from arid to perhumid.These patterns allow the development of conservation actions that respond to the presence of special places for plant diversification and of special species that require immediate attention. Further research will include the documentation of patterns at ever-finer spatial resolutions, to better match our biodiversity databases with the topographical and ecological features found in South America. The phylogenetics of plant molecular and morphological characters provide a necessary evolutionary framework that can then be compared to processes identified as important among animal and fungi lineages. For Andean South America, coevolution of plant and animal species is an important source of additional complexity, while trends of evolution to occupy drier and/or higher environments appear in numerous lineages. Anthropogenic influences on these patterns and processes are little understood, but humans have affected and will continue to shape the composition, diversity, and geography of South American biota.