This chapter reviews the history of the use of phylogenetics in ecology, beginning with a discussion of early attempts to classify the diversity of life and the development of evolutionary theory. In particular, it examines how early taxonomists, starting with Carl Linnaeus, have grouped species by similarity in their traits and how early ecologists and biologists such as Charles Darwin recognized the importance of relatedness in influencing ecological interactions and species distributions. The chapter proceeds by focusing on the introduction of the neutral theory of biodiversity into mainstream ecology and the development of the niche-based model of community assembly. It also considers how some ecologists questioned the relevance of phylogenetic corrections for ecology and concludes by analyzing the emergence of ecological phylogenetics or ecophylogenetics.