Abstract: One and half centuries ago, Charles Darwin (1859) argued that all living species shared common ancestors in the past, and Ernst Haeckel (1886) and other biologists in the late 1800's attempted to trace patterns of decent among all extant and extinct forms in what Darwin referred to as "the great Tree of Life." Ever since then, systematists and evolutionary biologists have been exploring historical information encoded in morphology and molecules, and actively developing theories and methods to infer phylogenetic relationships among organisms from this information. This endeavor has been especially stimulated by the rise of molecular biology and the emergence of computer science over the past 50 years. At the beginning of the 21st century, we are presented with an unprecedented opportunity to reconstruct the entire tree of life, and further, to study evolution in the context of a robust phylogenetic framework. Over the past decade, research on reconstructing the tree of life has been remarkably active, and knowledge is expanding exponentially (Cracraft and Donoghue, 2004; see also Pennisi 2003). On June 3-7, 2007, an international symposium on tree of life research was held in Beijing, China. It brought together some 20 leading speakers from Canada, Germany, Japan, New Zealand, Sweden, the U.K., and the U.S.A., and nearly 300 scientists from within China. This special issue of the Journal of Systematics and Evolution consists of 16 of the papers that were presented at the symposium. They represent a broad spectrum of research in systematics and evolutionary biology, ranging from exploration of theoretical issues, such as the effects of taxon and character sampling on phylogenetic analyses, to empirical studies and reviews of the use of multigene and whole genome analyses to infer the phylogeny of prokaryotes, protists, fungi, animals, and plants. These contributions also feature examples of the uses of phylogenetic approaches in studying historical biogeography, character evolution, and the evolutionary history of genes controlling chromosomal structural dynamics and development in eukaryotes. These papers provide an excellent sample of what can be expected in the future, as phylogenetic research becomes increasingly integrated with emerging fields in evolutionary biology, such as evolutionary developmental biology, evolutionary genomics, and evolutionary ecology. We have so much more to learn about how to harness the power of the phylogenetic knowledge that is materializing so rapidly, and we are excited about the prospects of developing a truly integrative phylogenetic biology over the coming decades. The symposium was financially supported by grants from the National Natural Science Foundation of China; the Chinese Academy of Sciences; the bioGENESIS core program within DIVERSITAS; the Japan Society for the Promotion of Science; the Jiangsu Institute of Botany, Jiangsu Province and the Chinese Academy of Sciences; the Institute of Zoology, Chinese Academy of Sciences; the Beijing Botanical Garden; the Institute of Botany, Chinese Academy of Sciences; the College of Life Sciences, Zhejiang University; and the School of Life Sciences, Fudan University. We are extremely grateful to all of these sponsors and delighted to present the outcome of their generous support in this special issue.