Phytochemical studies have experienced a great deal of change during the last century, not only regarding the number of compounds described, but also in the concept of phytochemistry itself. This change has mainly been related to two key points: the methodologies used in phytochemical studies and the questions regarding 'why secondary metabolites appeared in plants and in other living organisms?' and 'what is their role?'. This transformation in the field has led to new questions concerning such different subjects as evolution, paleobotany, biochemistry, plant physiology and ethnography. However, the main issue is to clarify the role that secondary metabolites play in the plant (and other organisms) and whether the resources invested in their production (C and N allocation, genes encoding their biogenetic pathways, specific enzymes, energy-rich molecules such as ATP and NADPH) have or lack a reasonable reward in terms of advantages for survival. Consequently, in this review the main emphasis will be placed on two subjects related to the evolution of phytochemical studies. The first aim is to describe briefly the influence that the development of the methodologies needed for compound isolation and structure elucidation have had on the field of phytochemistry. The second area to be covered concerns the new theories addressing the role of secondary metabolites from an ecological point of view: co-evolution of plants and their potential enemies (phytophagous insects, microbes, herbivores and other plants), chemical plant defence, adaptative strategies of phytophagues to plant toxins (among them sequestration will be briefly mentioned), and models and theories for carbon and nitrogen allocation. Some final remarks are made to summarize our opinion about the immediate future of phytochemical ecology and phytochemical studies.